ChemWiki - User contributions [en]

Mod:Hunt Research Group/hpc

2018-07-17T14:52:16Z

Mt1817: /* Recommended specifications */

=Running jobs on the Imperial HPC=
Back to the main [https://www.ch.ic.ac.uk/wiki/index.php/Mod:Hunt_Research_Group wiki-page]

== Queues to run on ==
:'''pqph''' (various, see below) this is the hunt group queue, runs on the servers listed below
::each user has can have a '''maximum of 12 running jobs'''
::to help balance usage please have a '''maximum of 20 jobs running or qued'''
:'''pqchem''' (42 nodes) this is the chemistry department queue,
:'''chemlab1''' (2 chassis) this is for the computational chemistry lab but can be used out of term time
:which can be accessed from https://scanweb.cc.ic.ac.uk/

== Using qstat ==
:qstat to get your jobs that are running
:qstat -q to get a list of all queues
:qdel and ID number to remove a job from the queue
:a short script to list all the queues in one command
::type qstatme and it will list the info for the three queues pqph, chemlab1 and pqchem
<pre>[phunt@login-3-internal]/home/phunt/bin $ cat qstatme
#!/bin/bash
#
qstat -q | grep 'pqph '
qstat -q | grep 'chemlab1 '
qstat -q | grep 'pqchem '
</pre>

== Submit script uses PBS queing==
*everyone should START by using this script, and not the automated submission script (see later)
*have a copy of this script in the directory you are running the job from
*here is an example called rng16_66
<pre>[phunt@login-3-internal]/work/phunt/ $ cat rng16_66
#!/bin/sh

# submit jobs to the que with this script using the following command:
# qsub -N jobname -v in=name rng16_66
# rng16_66 is this script
# jobname is a name you will see in the qstat command
# name is the actual file minus .com etc it is passed into this script as ${in}

# batch processing commands
#PBS -l walltime=119:59:00
#PBS -lselect=1:ncpus=16:mem=64000MB
#PBS -j oe
#PBS -q pqph

# load modules
#
module load gaussian/g09-d01

# check for a checkpoint file
#
# variable PBS_O_WORKDIR=directoiry from which the job was sumbited.
test -r $PBS_O_WORKDIR/${in}.chk
if [ $? -eq 0 ]
then
echo "located $PBS_O_WORKDIR/${in}.chk"
cp $PBS_O_WORKDIR/${in}.chk $TMPDIR/.
else
echo "no checkpoint file $PBS_O_WORKDIR/${in}.chk"
fi
#
# run gaussian
#
pbsexec g09 $PBS_O_WORKDIR/${in}.com
#
# job has ended copy back the checkpoint file
# check to see if there are other external files like .wfn or .mos and copy these as well
#
cp $TMPDIR/${in}.chk /$PBS_O_WORKDIR/.
test -r $TMPDIR/${in}.wfn
if [ $? -eq 0 ]
then
cp $TMPDIR/${in}.wfn /$PBS_O_WORKDIR/${in}.wfn
fi
test -r $TMPDIR/fort.7
if [ $? -eq 0 ]
then
cp $TMPDIR/fort.7 /$PBS_O_WORKDIR/${in}.mos
fi
# exit
</pre>

Without "#!/bin/sh" in the beginning of the job script, the job will always go to the queue "short" instead of the queue asked for.

==ONLY once you have used the queuing script for some time==
*use the gf script created by Giacommo made which makes it easier to submit jobs to the hpc.
*The link below contains the script and instructions for using it.
::https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Hunt_Research_Group/pimpQSUB

== Comments on the PBS ==
\#PBS -l walltime=119:59:00
*the -l walltime is the maximum time the job will run in seconds it will be killed at the walltime
*pqph has a very long walltime, other queues have a shorter walltime, adjust as necessary

\#PBS -q pqph
*the -q option tells it which queue to run on adjust as necessary

\#PBS -lselect=1:ncpus=16:mem=64000MB
*this is a very important line!
*lselect=1 means run on one node
*ncpus=the number of cpus
*mem=the maximum amount of memory
*these are specific to each node,
**it is important that you manage your usage properly to not waste resources and to allow efficient usage when there is a backlog of jobs
**decide on the size of your job, do you need many processors and lots of memory? if not run on a smaller node!
**use [https://www.hpc.imperial.ac.uk/selfservice/cx1/pqadmin/pqph/nodes nodes] to select which node you want to run on
**set the ncpus and mem appropriately (see below)
**note that you cannot use as much memory as is indicated in the Node status table, always request slightly less
*sometimes the job does not go in properly if you use GB so always use MB in your specification
**1GB=1000MB

\#PBS -j oe
•merge the standard output and error files

== Memory needed to run ==

*Gaussian is greedy and will exceed the allocated memory
:: each proc needs a gaussian executable, which takes about 8MW (or 12 for MP2 frequencies)
::MW is megaword which is the unit gaussian allocates memory
::1MW is about 8.4MB
:::so each proc needs 1*8*8.4 approximately 68MB just to run
:::so 12 proc jobs require 12*68=816MB just to run
:::so 16 proc jobs require 16*68=1088MB just to run
:::so 20 proc jobs require 20*68=1360MB just to run
:::so 24 proc jobs require 24*68=1632MB just to run
:::so 40 proc jobs require 40*68=2720MB just to run
:::so 48 proc jobs require 48*68=3264MB just to run
::so when allocating memory inside the gaussian job you must reduce the memory by at least this amount
*thus best to reduce the memory by about 100MB*no.processors inside the gaussian script
*you also need some overhead within the PBS script

*the memory can be given in binary such as 251 GB (binary) is really 251 GB =251000*1,048,576 Bytes =264GB (decimal)

== Recommended specifications ==

in the following
: the first line gives the processor and memory
: the second line the amount to allocate in the PBS script
: the third and fourth lines the amount to allocated in the gaussian com file

:'''Small jobs''' use half a 24proc node: 12 cpu 47 GB
::\#PBS -lselect=1:ncpus=12:mem=46000MB
::%nprocs=12
::%mem=45000MB

:'''Medium jobs''' 7 nodes: 32 cpu 62 GB
::\#PBS -lselect=1:ncpus=32:mem=61000MB
::%nprocs=32
::%mem=58000MB

:'''Medium jobs''' 12 nodes: 24 cpu 92 GB
::\#PBS -lselect=1:ncpus=24:mem=91000MB
::%nprocs=24
::%mem=88000MB

:'''Large jobs''' 7 nodes: 40 cpu 125 GB
::\#PBS -lselect=1:ncpus=40:mem=124000MB
::%nprocs=40
::%mem=120000MB

:'''Largest jobs''' 4 nodes: 48 cpu 256 GB
::\#PBS -lselect=1:ncpus=48:mem=255000MB
::%nprocs=48
::%mem=250000MB

*add tmpspace=400 only for large disk jobs to ensure you are put on a node with enough disk!!
*Note that this requires you to include maxdisk=400gb in your gaussian input.
:NOTE the queing system does not check disk allocations. When requesting large disk jobs remember to request all of the processors on a node even if you are not using all of the processors. For large jobs the maximum disk space you can request is '''800GB''' on the 12 processor nodes.

==more details for if you seem to be having memory or disk issues==
*normal jobs
::will need 2*N^2 W *8.4 to get B (1,048,576B =1MB)
:: so 300 basis functions will need 180000W =0.18MW =1.5MB in addition to the above requirements
::require 2ON^2 W of disk to run where O=number of occupied orbitals, N=number of basis functions

*MP2 jobs
:: work best with %mem and maxdisk defined
:: in-core requires N^4/4 divided by 1,000,000 MW memory
:: so 400 basis functions will need 6400MW=53760MB=54GB memory per node, which is unlikely!
:: semi-direct requires 2*O(N^2) memory and N^3 disk
:: so N=476 basis functions O=56 occupied orbitals will need
::25.4MW=214MB of memory
::and 108MW=906MB disk (this is not actually true it will need much more probably around 1800MB disk per processor!)
::so total memory for MP2 freq 8proc will be
::12*8*8.4=807MB to run and 8*214=1712MB for calcs and some extra 400MB=3019MB=3.3GB
::gaussian does not like GB directive so give %mem in MB

== checkpoint and other files ==
: checkpoint files should be exactly the same name as the input file name
: for jobs that may exceed the wall time specify the full path of the checkpoint file, for example
::%chk=/work/phunt/tmp/filename.chk
:this means the checkpoint file will be written into your personal work directory, it may slow the job down
:this is also the reason /work is sometimes very slow on CX1 so only do this as an exception!

== Other information (may be out of date) ==
:3.1 CPMD:
::https://www.ch.ic.ac.uk/wiki/index.php/Image:Runcpmd_md.sh
:3.2 DL-POLY:
::https://www.ch.ic.ac.uk/wiki/index.php/Image:Mpirun.sh
::Note: You´ll not be able to see the output until the job finishes : the directory /tmp/pb.XXX isn´t accessible to you because it is on the private disk of the node running the job.
::To get DLPOLY to terminate before the job hits the walltime limit and killed, you need to run it through a program called pbsexec, for example:
::pbsexec mpiexec DLPOLY.X
::This will kill DLPOLY 15 minutes before the walltime limit, giving your script time to transfer files back to $work.

Talk:Mod:Hunt Research Group/How to draw SDFs with TRAVIS

2018-03-25T11:51:10Z

Mt1817:

TRAVIS is a free tool for analyzing and visualizing trajectories from MD simulations.

TRAVIS source code can be obtained for free from "Source Code (.tar.gz)" at Download page on TRAVIS website.[http://www.travis-analyzer.de/]
How to compile and Install TRAVIS is explained on Page 3 in "Quick Start Guide (PDF)" which can be downloaded on the same link.

Details about TRAVIS is explained in the paper.[https://pubs.acs.org/doi/abs/10.1021/ci200217w]
M. Brehm and B. Kirchner. J. Chem. Inf. Model. 2011, 51 (8), pp 2007-2023.

Manual in Word format is obtained here. [[How to generate SDF.docx]]
*[N1444][NTf2] HISTORY(trajectory) file for trial use is here. [[Media:HISTORY.txt]]
*NB: When you use this file with TRAVIS, change the file name from HISTORY.txt to HISTORY before using. [N1444][NTf2]= tri-n-butylmethylammonium bis-(trifluoromethanesulfonyl)imide (Fig. 1)

----
'''How to draw SDFs with TRAVIS'''
*The explanation below is written to explain how to draw spatial distribution of anions in the first shell around a cation by using [N1444][NTf2] as an example.

[[File:SDF 1.jpg]]

1. Create a new directory and put HISTORY file there.
*HISTORY file is so huge that it takes much time to copy. It is recommended to make a link from the original location by executing “ln -s (Original location)/HISTORY HISTORY” in the created directory.

2. Execute “travis HISTORY” in the created directory, and answer the displayed questions based on your model (and preference). Default answers are shown in brackets and when you choose the default answers, just type Enter. Questions and answers shown below are based on [N1444][NTf2].
[[File:SDF 2.jpg]]

After answering “Create images of the structural formulas?”, press “Ctrl” and “c” at the same to quit once.
Then, execute “ls -l”, and you will find “.dot” files.
[[File:SDF 3.jpg]]

3. Visualise the “.dot” files. Choose from the options below.

3-1. Using Graphviz (Recommended)
Visit https:/www.graphviz.org/download/ and download Graphviz.

Then, execute “neato -Tpng mol1_****.dot -o mol1_***.png”.

In [N1444][NTf2] example, execute “neato -Tpng mol1_C2F6NO4S2.dot -o mol1_C2F6NO4S2.png”.

Likewise, execute “neato -Tpng mol2_****.dot -o mol2_***.png”.

In [N1444][NTf2] example, execute “neato -Tpng mol1_C13H30N.dot -o mol1_C13H30N.png”.

When you execute “ls -l”, you will find two png files. After sending these png files to your local machine, open them and confirm the chemical structures.

In [N1444][NTf2] example, you will find the structure shown in Fig 1.

3-2. Handwriting the chemical structure (Recommended only if the structure is simple)
In the screen, you will find “bond matrices” shown as below. Thus, you can handwrite the chemical structure based on this information.
For example, the matrices below mean C1 is bonded to F4, F5, F6, and S1.
[[File:SDF 4.jpg]]

4. Return to the directory created in Step 1, and execute “travis HISTORY” again. Restart answering the questions. When you face “Create images of the structural formulas?”, answer no (just type Enter) this time, and keep answering until the end.
[[File:SDF 5.jpg]]

5. When you finish answering all questions, TRAVIS starts creating SDF files. W ait until ***The End*** is shown. Then, execute “ls -l”, and you will find the created files. Send SDF files(.plt) and ref file to your local machine.
[[File:SDF 6.jpg]]

6. Start VMD. Open your SDF by following the instruction below.
[[File:SDF 7.jpg]]

(Options)
6-1. Change the SDF graphics based on your preference.
[[File:SDF 8.jpg]]

6-2. Change the background colour based on your preference.
[[File:SDF 9.jpg]]

6-3. Change the input file based on your preference.
[[File:SDF 10.jpg]]

7. Insert the reference molecule (cation) by following the instruction below.
[[File:SDF 11.jpg]]

Talk:Mod:Hunt Research Group/How to draw SDFs with TRAVIS

2018-03-25T11:50:18Z

Mt1817:

TRAVIS is a free tool for analyzing and visualizing trajectories from MD simulations.

TRAVIS source code can be obtained for free from "Source Code (.tar.gz)" at Download page on TRAVIS website.[http://www.travis-analyzer.de/]
How to compile and Install TRAVIS is explained on Page 3 in "Quick Start Guide (PDF)" which can be downloaded on the same link.

Details about TRAVIS is explained in the paper.[https://pubs.acs.org/doi/abs/10.1021/ci200217w]
M. Brehm and B. Kirchner. J. Chem. Inf. Model. 2011, 51 (8), pp 2007-2023.

Manual in Word format is obtained here:How to generate SDF.docx]]
*[N1444][NTf2] HISTORY(trajectory) file for trial use is here. [[Media:HISTORY.txt]]
*NB: When you use this file with TRAVIS, change the file name from HISTORY.txt to HISTORY before using. [N1444][NTf2]= tri-n-butylmethylammonium bis-(trifluoromethanesulfonyl)imide (Fig. 1)

----
'''How to draw SDFs with TRAVIS'''
*The explanation below is written to explain how to draw spatial distribution of anions in the first shell around a cation by using [N1444][NTf2] as an example.

[[File:SDF 1.jpg]]

1. Create a new directory and put HISTORY file there.
*HISTORY file is so huge that it takes much time to copy. It is recommended to make a link from the original location by executing “ln -s (Original location)/HISTORY HISTORY” in the created directory.

2. Execute “travis HISTORY” in the created directory, and answer the displayed questions based on your model (and preference). Default answers are shown in brackets and when you choose the default answers, just type Enter. Questions and answers shown below are based on [N1444][NTf2].
[[File:SDF 2.jpg]]

After answering “Create images of the structural formulas?”, press “Ctrl” and “c” at the same to quit once.
Then, execute “ls -l”, and you will find “.dot” files.
[[File:SDF 3.jpg]]

3. Visualise the “.dot” files. Choose from the options below.

3-1. Using Graphviz (Recommended)
Visit https:/www.graphviz.org/download/ and download Graphviz.

Then, execute “neato -Tpng mol1_****.dot -o mol1_***.png”.

In [N1444][NTf2] example, execute “neato -Tpng mol1_C2F6NO4S2.dot -o mol1_C2F6NO4S2.png”.

Likewise, execute “neato -Tpng mol2_****.dot -o mol2_***.png”.

In [N1444][NTf2] example, execute “neato -Tpng mol1_C13H30N.dot -o mol1_C13H30N.png”.

When you execute “ls -l”, you will find two png files. After sending these png files to your local machine, open them and confirm the chemical structures.

In [N1444][NTf2] example, you will find the structure shown in Fig 1.

3-2. Handwriting the chemical structure (Recommended only if the structure is simple)
In the screen, you will find “bond matrices” shown as below. Thus, you can handwrite the chemical structure based on this information.
For example, the matrices below mean C1 is bonded to F4, F5, F6, and S1.
[[File:SDF 4.jpg]]

4. Return to the directory created in Step 1, and execute “travis HISTORY” again. Restart answering the questions. When you face “Create images of the structural formulas?”, answer no (just type Enter) this time, and keep answering until the end.
[[File:SDF 5.jpg]]

5. When you finish answering all questions, TRAVIS starts creating SDF files. W ait until ***The End*** is shown. Then, execute “ls -l”, and you will find the created files. Send SDF files(.plt) and ref file to your local machine.
[[File:SDF 6.jpg]]

6. Start VMD. Open your SDF by following the instruction below.
[[File:SDF 7.jpg]]

(Options)
6-1. Change the SDF graphics based on your preference.
[[File:SDF 8.jpg]]

6-2. Change the background colour based on your preference.
[[File:SDF 9.jpg]]

6-3. Change the input file based on your preference.
[[File:SDF 10.jpg]]

7. Insert the reference molecule (cation) by following the instruction below.
[[File:SDF 11.jpg]]

File:How to generate SDF.docx

2018-03-25T11:50:13Z

Mt1817: Mt1817 uploaded a new version of File:How to generate SDF.docx

File:SDF 11.jpg

2018-03-25T11:48:10Z

Mt1817:

Talk:Mod:Hunt Research Group/How to draw SDFs with TRAVIS

2018-03-25T11:46:01Z

Mt1817:

TRAVIS is a free tool for analyzing and visualizing trajectories from MD simulations.

TRAVIS source code can be obtained for free from "Source Code (.tar.gz)" at Download page on TRAVIS website.[http://www.travis-analyzer.de/]
How to compile and Install TRAVIS is explained on Page 3 in "Quick Start Guide (PDF)" which can be downloaded on the same link.

Details about TRAVIS is explained in the paper.[https://pubs.acs.org/doi/abs/10.1021/ci200217w]
M. Brehm and B. Kirchner. J. Chem. Inf. Model. 2011, 51 (8), pp 2007-2023.

Manual in Word format is obtained here:How to generate SDF.docx]]
*[N1444][NTf2] HISTORY(trajectory) file for trial use is here. [[Media:HISTORY.txt]]
*NB: When you use this file with TRAVIS, change the file name from HISTORY.txt to HISTORY before using. [N1444][NTf2]= tri-n-butylmethylammonium bis-(trifluoromethanesulfonyl)imide (Fig. 1)

----
'''How to draw SDFs with TRAVIS'''
*The explanation below is written to explain how to draw spatial distribution of anions in the first shell around a cation by using [N1444][NTf2] as an example.

[[File:SDF 1.jpg]]

1. Create a new directory and put HISTORY file there.
*HISTORY file is so huge that it takes much time to copy. It is recommended to make a link from the original location by executing “ln -s (Original location)/HISTORY HISTORY” in the created directory.

2. Execute “travis HISTORY” in the created directory, and answer the displayed questions based on your model (and preference). Default answers are shown in brackets and when you choose the default answers, just type Enter. Questions and answers shown below are based on [N1444][NTf2].
[[File:SDF 2.jpg]]

After answering “Create images of the structural formulas?”, press “Ctrl” and “c” at the same to quit once.
Then, execute “ls -l”, and you will find “.dot” files.
[[File:SDF 3.jpg]]

3. Visualise the “.dot” files. Choose from the options below.

3-1. Using Graphviz (Recommended)
Visit https:/www.graphviz.org/download/ and download Graphviz.

Then, execute “neato -Tpng mol1_****.dot -o mol1_***.png”.

In [N1444][NTf2] example, execute “neato -Tpng mol1_C2F6NO4S2.dot -o mol1_C2F6NO4S2.png”.

Likewise, execute “neato -Tpng mol2_****.dot -o mol2_***.png”.

In [N1444][NTf2] example, execute “neato -Tpng mol1_C13H30N.dot -o mol1_C13H30N.png”.

When you execute “ls -l”, you will find two png files. After sending these png files to your local machine, open them and confirm the chemical structures.

In [N1444][NTf2] example, you will find the structure shown in Fig 1.

3-2. Handwriting the chemical structure (Recommended only if the structure is simple)
In the screen, you will find “bond matrices” shown as below. Thus, you can handwrite the chemical structure based on this information.
For example, the matrices below mean C1 is bonded to F4, F5, F6, and S1.
[[File:SDF 4.jpg]]

4. Return to the directory created in Step 1, and execute “travis HISTORY” again. Restart answering the questions. When you face “Create images of the structural formulas?”, answer no (just type Enter) this time, and keep answering until the end.
[[File:SDF 5.jpg]]

5. When you finish answering all questions, TRAVIS starts creating SDF files. W ait until ***The End*** is shown. Then, execute “ls -l”, and you will find the created files. Send SDF files(.plt) and ref file to your local machine.
[[File:SDF 6.jpg]]

6. Start VMD. Open your SDF by following the instruction below.
[[File:SDF 7.jpg]]

(Options)
6-1. Change the SDF graphics based on your preference.
[[File:SDF 8.jpg]]

6-2. Change the background colour based on your preference.
[[File:SDF 9.jpg]]

6-3. Change the input file based on your preference.
[[File:SDF 10.jpg]]

7. Insert the reference molecule (cation) by following the instruction below.

File:SDF 10.jpg

2018-03-25T11:45:42Z

Mt1817:

File:SDF 9.jpg

2018-03-25T11:44:44Z

Mt1817:

File:SDF 8.jpg

2018-03-25T11:43:09Z

Mt1817:

Talk:Mod:Hunt Research Group/How to draw SDFs with TRAVIS

2018-03-25T11:42:31Z

Mt1817:

TRAVIS is a free tool for analyzing and visualizing trajectories from MD simulations.

TRAVIS source code can be obtained for free from "Source Code (.tar.gz)" at Download page on TRAVIS website.[http://www.travis-analyzer.de/]
How to compile and Install TRAVIS is explained on Page 3 in "Quick Start Guide (PDF)" which can be downloaded on the same link.

Details about TRAVIS is explained in the paper.[https://pubs.acs.org/doi/abs/10.1021/ci200217w]
M. Brehm and B. Kirchner. J. Chem. Inf. Model. 2011, 51 (8), pp 2007-2023.

Manual in Word format is obtained here:How to generate SDF.docx]]
*[N1444][NTf2] HISTORY(trajectory) file for trial use is here. [[Media:HISTORY.txt]]
*NB: When you use this file with TRAVIS, change the file name from HISTORY.txt to HISTORY before using. [N1444][NTf2]= tri-n-butylmethylammonium bis-(trifluoromethanesulfonyl)imide (Fig. 1)

----
'''How to draw SDFs with TRAVIS'''
*The explanation below is written to explain how to draw spatial distribution of anions in the first shell around a cation by using [N1444][NTf2] as an example.

[[File:SDF 1.jpg]]

1. Create a new directory and put HISTORY file there.
*HISTORY file is so huge that it takes much time to copy. It is recommended to make a link from the original location by executing “ln -s (Original location)/HISTORY HISTORY” in the created directory.

2. Execute “travis HISTORY” in the created directory, and answer the displayed questions based on your model (and preference). Default answers are shown in brackets and when you choose the default answers, just type Enter. Questions and answers shown below are based on [N1444][NTf2].
[[File:SDF 2.jpg]]

After answering “Create images of the structural formulas?”, press “Ctrl” and “c” at the same to quit once.
Then, execute “ls -l”, and you will find “.dot” files.
[[File:SDF 3.jpg]]

3. Visualise the “.dot” files. Choose from the options below.

3-1. Using Graphviz (Recommended)
Visit https:/www.graphviz.org/download/ and download Graphviz.

Then, execute “neato -Tpng mol1_****.dot -o mol1_***.png”.

In [N1444][NTf2] example, execute “neato -Tpng mol1_C2F6NO4S2.dot -o mol1_C2F6NO4S2.png”.

Likewise, execute “neato -Tpng mol2_****.dot -o mol2_***.png”.

In [N1444][NTf2] example, execute “neato -Tpng mol1_C13H30N.dot -o mol1_C13H30N.png”.

When you execute “ls -l”, you will find two png files. After sending these png files to your local machine, open them and confirm the chemical structures.

In [N1444][NTf2] example, you will find the structure shown in Fig 1.

3-2. Handwriting the chemical structure (Recommended only if the structure is simple)
In the screen, you will find “bond matrices” shown as below. Thus, you can handwrite the chemical structure based on this information.
For example, the matrices below mean C1 is bonded to F4, F5, F6, and S1.
[[File:SDF 4.jpg]]

4. Return to the directory created in Step 1, and execute “travis HISTORY” again. Restart answering the questions. When you face “Create images of the structural formulas?”, answer no (just type Enter) this time, and keep answering until the end.
[[File:SDF 5.jpg]]

5. When you finish answering all questions, TRAVIS starts creating SDF files. W ait until ***The End*** is shown. Then, execute “ls -l”, and you will find the created files. Send SDF files(.plt) and ref file to your local machine.
[[File:SDF 6.jpg]]

6. Start VMD. Open your SDF by following the instruction below.
[[File:SDF 7.jpg]]

(Options)
6-1. Change the SDF graphics based on your preference.
[[File:SDF 8.jpg]]

6-2. Change the background colour based on your preference.

Talk:Mod:Hunt Research Group/How to draw SDFs with TRAVIS

2018-03-25T11:40:32Z

Mt1817:

TRAVIS is a free tool for analyzing and visualizing trajectories from MD simulations.

TRAVIS source code can be obtained for free from "Source Code (.tar.gz)" at Download page on TRAVIS website.[http://www.travis-analyzer.de/]
How to compile and Install TRAVIS is explained on Page 3 in "Quick Start Guide (PDF)" which can be downloaded on the same link.

Details about TRAVIS is explained in the paper.[https://pubs.acs.org/doi/abs/10.1021/ci200217w]
M. Brehm and B. Kirchner. J. Chem. Inf. Model. 2011, 51 (8), pp 2007-2023.

Manual in Word format is obtained here:How to generate SDF.docx]]
*[N1444][NTf2] HISTORY(trajectory) file for trial use is here. [[Media:HISTORY.txt]]
*NB: When you use this file with TRAVIS, change the file name from HISTORY.txt to HISTORY before using. [N1444][NTf2]= tri-n-butylmethylammonium bis-(trifluoromethanesulfonyl)imide (Fig. 1)

----
'''How to draw SDFs with TRAVIS'''
*The explanation below is written to explain how to draw spatial distribution of anions in the first shell around a cation by using [N1444][NTf2] as an example.

[[File:SDF 1.jpg]]

1. Create a new directory and put HISTORY file there.
*HISTORY file is so huge that it takes much time to copy. It is recommended to make a link from the original location by executing “ln -s (Original location)/HISTORY HISTORY” in the created directory.

2. Execute “travis HISTORY” in the created directory, and answer the displayed questions based on your model (and preference). Default answers are shown in brackets and when you choose the default answers, just type Enter. Questions and answers shown below are based on [N1444][NTf2].
[[File:SDF 2.jpg]]

After answering “Create images of the structural formulas?”, press “Ctrl” and “c” at the same to quit once.
Then, execute “ls -l”, and you will find “.dot” files.
[[File:SDF 3.jpg]]

3. Visualise the “.dot” files. Choose from the options below.

3-1. Using Graphviz (Recommended)
Visit https:/www.graphviz.org/download/ and download Graphviz.

Then, execute “neato -Tpng mol1_****.dot -o mol1_***.png”.

In [N1444][NTf2] example, execute “neato -Tpng mol1_C2F6NO4S2.dot -o mol1_C2F6NO4S2.png”.

Likewise, execute “neato -Tpng mol2_****.dot -o mol2_***.png”.

In [N1444][NTf2] example, execute “neato -Tpng mol1_C13H30N.dot -o mol1_C13H30N.png”.

When you execute “ls -l”, you will find two png files. After sending these png files to your local machine, open them and confirm the chemical structures.

In [N1444][NTf2] example, you will find the structure shown in Fig 1.

3-2. Handwriting the chemical structure (Recommended only if the structure is simple)
In the screen, you will find “bond matrices” shown as below. Thus, you can handwrite the chemical structure based on this information.
For example, the matrices below mean C1 is bonded to F4, F5, F6, and S1.
[[File:SDF 4.jpg]]

4. Return to the directory created in Step 1, and execute “travis HISTORY” again. Restart answering the questions. When you face “Create images of the structural formulas?”, answer no (just type Enter) this time, and keep answering until the end.
[[File:SDF 5.jpg]]

5. When you finish answering all questions, TRAVIS starts creating SDF files. W ait until ***The End*** is shown. Then, execute “ls -l”, and you will find the created files. Send SDF files(.plt) and ref file to your local machine.
[[File:SDF 6.jpg]]

6. Start VMD. Open your SDF by following the instruction below.
[[File:SDF 7.jpg]]

(Options)
6-1. Change the SDF graphics based on your preference.

File:SDF 7.jpg

2018-03-25T11:39:52Z

Mt1817:

File:SDF 6.jpg

2018-03-25T11:38:41Z

Mt1817:

Talk:Mod:Hunt Research Group/How to draw SDFs with TRAVIS

2018-03-25T11:38:07Z

Mt1817:

TRAVIS is a free tool for analyzing and visualizing trajectories from MD simulations.

TRAVIS source code can be obtained for free from "Source Code (.tar.gz)" at Download page on TRAVIS website.[http://www.travis-analyzer.de/]
How to compile and Install TRAVIS is explained on Page 3 in "Quick Start Guide (PDF)" which can be downloaded on the same link.

Details about TRAVIS is explained in the paper.[https://pubs.acs.org/doi/abs/10.1021/ci200217w]
M. Brehm and B. Kirchner. J. Chem. Inf. Model. 2011, 51 (8), pp 2007-2023.

Manual in Word format is obtained here:How to generate SDF.docx]]
*[N1444][NTf2] HISTORY(trajectory) file for trial use is here. [[Media:HISTORY.txt]]
*NB: When you use this file with TRAVIS, change the file name from HISTORY.txt to HISTORY before using. [N1444][NTf2]= tri-n-butylmethylammonium bis-(trifluoromethanesulfonyl)imide (Fig. 1)

----
'''How to draw SDFs with TRAVIS'''
*The explanation below is written to explain how to draw spatial distribution of anions in the first shell around a cation by using [N1444][NTf2] as an example.

[[File:SDF 1.jpg]]

1. Create a new directory and put HISTORY file there.
*HISTORY file is so huge that it takes much time to copy. It is recommended to make a link from the original location by executing “ln -s (Original location)/HISTORY HISTORY” in the created directory.

2. Execute “travis HISTORY” in the created directory, and answer the displayed questions based on your model (and preference). Default answers are shown in brackets and when you choose the default answers, just type Enter. Questions and answers shown below are based on [N1444][NTf2].
[[File:SDF 2.jpg]]

After answering “Create images of the structural formulas?”, press “Ctrl” and “c” at the same to quit once.
Then, execute “ls -l”, and you will find “.dot” files.
[[File:SDF 3.jpg]]

3. Visualise the “.dot” files. Choose from the options below.

3-1. Using Graphviz (Recommended)
Visit https:/www.graphviz.org/download/ and download Graphviz.

Then, execute “neato -Tpng mol1_****.dot -o mol1_***.png”.

In [N1444][NTf2] example, execute “neato -Tpng mol1_C2F6NO4S2.dot -o mol1_C2F6NO4S2.png”.

Likewise, execute “neato -Tpng mol2_****.dot -o mol2_***.png”.

In [N1444][NTf2] example, execute “neato -Tpng mol1_C13H30N.dot -o mol1_C13H30N.png”.

When you execute “ls -l”, you will find two png files. After sending these png files to your local machine, open them and confirm the chemical structures.

In [N1444][NTf2] example, you will find the structure shown in Fig 1.

3-2. Handwriting the chemical structure (Recommended only if the structure is simple)
In the screen, you will find “bond matrices” shown as below. Thus, you can handwrite the chemical structure based on this information.
For example, the matrices below mean C1 is bonded to F4, F5, F6, and S1.
[[File:SDF 4.jpg]]

4. Return to the directory created in Step 1, and execute “travis HISTORY” again. Restart answering the questions. When you face “Create images of the structural formulas?”, answer no (just type Enter) this time, and keep answering until the end.
[[File:SDF 5.jpg]]

5. When you finish answering all questions, TRAVIS starts creating SDF files. W ait until ***The End*** is shown. Then, execute “ls -l”, and you will find the created files. Send SDF files(.plt) and ref file to your local machine.
[[File:SDF 6.jpg]]

6. Start VMD. Open your SDF by following the instruction below.

Talk:Mod:Hunt Research Group/How to draw SDFs with TRAVIS

2018-03-25T11:35:12Z

Mt1817:

TRAVIS is a free tool for analyzing and visualizing trajectories from MD simulations.

TRAVIS source code can be obtained for free from "Source Code (.tar.gz)" at Download page on TRAVIS website.[http://www.travis-analyzer.de/]
How to compile and Install TRAVIS is explained on Page 3 in "Quick Start Guide (PDF)" which can be downloaded on the same link.

Details about TRAVIS is explained in the paper.[https://pubs.acs.org/doi/abs/10.1021/ci200217w]
M. Brehm and B. Kirchner. J. Chem. Inf. Model. 2011, 51 (8), pp 2007-2023.

Manual in Word format is obtained here:How to generate SDF.docx]]
*[N1444][NTf2] HISTORY(trajectory) file for trial use is here. [[Media:HISTORY.txt]]
*NB: When you use this file with TRAVIS, change the file name from HISTORY.txt to HISTORY before using. [N1444][NTf2]= tri-n-butylmethylammonium bis-(trifluoromethanesulfonyl)imide (Fig. 1)

----
'''How to draw SDFs with TRAVIS'''
*The explanation below is written to explain how to draw spatial distribution of anions in the first shell around a cation by using [N1444][NTf2] as an example.

[[File:SDF 1.jpg]]

1. Create a new directory and put HISTORY file there.
*HISTORY file is so huge that it takes much time to copy. It is recommended to make a link from the original location by executing “ln -s (Original location)/HISTORY HISTORY” in the created directory.

2. Execute “travis HISTORY” in the created directory, and answer the displayed questions based on your model (and preference). Default answers are shown in brackets and when you choose the default answers, just type Enter. Questions and answers shown below are based on [N1444][NTf2].
[[File:SDF 2.jpg]]

After answering “Create images of the structural formulas?”, press “Ctrl” and “c” at the same to quit once.
Then, execute “ls -l”, and you will find “.dot” files.
[[File:SDF 3.jpg]]

3. Visualise the “.dot” files. Choose from the options below.

3-1. Using Graphviz (Recommended)
Visit https:/www.graphviz.org/download/ and download Graphviz.

Then, execute “neato -Tpng mol1_****.dot -o mol1_***.png”.

In [N1444][NTf2] example, execute “neato -Tpng mol1_C2F6NO4S2.dot -o mol1_C2F6NO4S2.png”.

Likewise, execute “neato -Tpng mol2_****.dot -o mol2_***.png”.

In [N1444][NTf2] example, execute “neato -Tpng mol1_C13H30N.dot -o mol1_C13H30N.png”.

When you execute “ls -l”, you will find two png files. After sending these png files to your local machine, open them and confirm the chemical structures.

In [N1444][NTf2] example, you will find the structure shown in Fig 1.

3-2. Handwriting the chemical structure (Recommended only if the structure is simple)
In the screen, you will find “bond matrices” shown as below. Thus, you can handwrite the chemical structure based on this information.
For example, the matrices below mean C1 is bonded to F4, F5, F6, and S1.
[[File:SDF 4.jpg]]

4. Return to the directory created in Step 1, and execute “travis HISTORY” again. Restart answering the questions. When you face “Create images of the structural formulas?”, answer no (just type Enter) this time, and keep answering until the end.
[[File:SDF 5.jpg]]

5. When you finish answering all questions, TRAVIS starts creating SDF files. W ait until ***The End*** is shown. Then, execute “ls -l”, and you will find the created files. Send SDF files(.plt) and ref file to your local machine.

Talk:Mod:Hunt Research Group/How to draw SDFs with TRAVIS

2018-03-25T11:34:07Z

Mt1817:

TRAVIS is a free tool for analyzing and visualizing trajectories from MD simulations.

TRAVIS source code can be obtained for free from "Source Code (.tar.gz)" at Download page on TRAVIS website.[http://www.travis-analyzer.de/]
How to compile and Install TRAVIS is explained on Page 3 in "Quick Start Guide (PDF)" which can be downloaded on the same link.

Details about TRAVIS is explained in the paper.[https://pubs.acs.org/doi/abs/10.1021/ci200217w]
M. Brehm and B. Kirchner. J. Chem. Inf. Model. 2011, 51 (8), pp 2007-2023.

Manual in Word format is obtained here:How to generate SDF.docx]]
*[N1444][NTf2] HISTORY(trajectory) file for trial use is here. [[Media:HISTORY.txt]]
*NB: When you use this file with TRAVIS, change the file name from HISTORY.txt to HISTORY before using. [N1444][NTf2]= tri-n-butylmethylammonium bis-(trifluoromethanesulfonyl)imide (Fig. 1)

----
'''How to draw SDFs with TRAVIS'''
*The explanation below is written to explain how to draw spatial distribution of anions in the first shell around a cation by using [N1444][NTf2] as an example.

[[File:SDF 1.jpg]]

1. Create a new directory and put HISTORY file there.
*HISTORY file is so huge that it takes much time to copy. It is recommended to make a link from the original location by executing “ln -s (Original location)/HISTORY HISTORY” in the created directory.

2. Execute “travis HISTORY” in the created directory, and answer the displayed questions based on your model (and preference). Default answers are shown in brackets and when you choose the default answers, just type Enter. Questions and answers shown below are based on [N1444][NTf2].
[[File:SDF 2.jpg]]

After answering “Create images of the structural formulas?”, press “Ctrl” and “c” at the same to quit once.
Then, execute “ls -l”, and you will find “.dot” files.
[[File:SDF 3.jpg]]

3. Visualise the “.dot” files. Choose from the options below.

3-1. Using Graphviz (Recommended)
Visit https:/www.graphviz.org/download/ and download Graphviz.

Then, execute “neato -Tpng mol1_****.dot -o mol1_***.png”.
In [N1444][NTf2] example, execute “neato -Tpng mol1_C2F6NO4S2.dot -o mol1_C2F6NO4S2.png”.

Likewise, execute “neato -Tpng mol2_****.dot -o mol2_***.png”.

In [N1444][NTf2] example, execute “neato -Tpng mol1_C13H30N.dot -o mol1_C13H30N.png”.

When you execute “ls -l”, you will find two png files. After sending these png files to your local machine, open them and confirm the chemical structures.

In [N1444][NTf2] example, you will find the structure shown in Fig 1.

3-2. Handwriting the chemical structure (Recommended only if the structure is simple)
In the screen, you will find “bond matrices” shown as below. Thus, you can handwrite the chemical structure based on this information.
For example, the matrices below mean C1 is bonded to F4, F5, F6, and S1.
[[File:SDF 4.jpg]]

4. Return to the directory created in Step 1, and execute “travis HISTORY” again. Restart answering the questions. When you face “Create images of the structural formulas?”, answer no (just type Enter) this time, and keep answering until the end.
[[File:SDF 5.jpg]]

5. When you finish answering all questions, TRAVIS starts creating SDF files. W ait until ***The End*** is shown. Then, execute “ls -l”, and you will find the created files. Send SDF files(.plt) and ref file to your local machine.

Talk:Mod:Hunt Research Group/How to draw SDFs with TRAVIS

2018-03-25T11:33:18Z

Mt1817:

TRAVIS is a free tool for analyzing and visualizing trajectories from MD simulations.

TRAVIS source code can be obtained for free from "Source Code (.tar.gz)" at Download page on TRAVIS website.[http://www.travis-analyzer.de/]
How to compile and Install TRAVIS is explained on Page 3 in "Quick Start Guide (PDF)" which can be downloaded on the same link.

Details about TRAVIS is explained in the paper.[https://pubs.acs.org/doi/abs/10.1021/ci200217w]
M. Brehm and B. Kirchner. J. Chem. Inf. Model. 2011, 51 (8), pp 2007-2023.

Manual in Word format is obtained here:How to generate SDF.docx]]
*[N1444][NTf2] HISTORY(trajectory) file for trial use is here. [[Media:HISTORY.txt]]
*NB: When you use this file with TRAVIS, change the file name from HISTORY.txt to HISTORY before using. [N1444][NTf2]= tri-n-butylmethylammonium bis-(trifluoromethanesulfonyl)imide (Fig. 1)

----
'''How to draw SDFs with TRAVIS'''
*The explanation below is written to explain how to draw spatial distribution of anions in the first shell around a cation by using [N1444][NTf2] as an example.

[[File:SDF 1.jpg]]

1. Create a new directory and put HISTORY file there.
*HISTORY file is so huge that it takes much time to copy. It is recommended to make a link from the original location by executing “ln -s (Original location)/HISTORY HISTORY” in the created directory.

2. Execute “travis HISTORY” in the created directory, and answer the displayed questions based on your model (and preference). Default answers are shown in brackets and when you choose the default answers, just type Enter. Questions and answers shown below are based on [N1444][NTf2].
[[File:SDF 2.jpg]]

After answering “Create images of the structural formulas?”, press “Ctrl” and “c” at the same to quit once.
Then, execute “ls -l”, and you will find “.dot” files.
[[File:SDF 3.jpg]]

3. Visualise the “.dot” files. Choose from the options below.

3-1. Using Graphviz (Recommended)
Visit https:/www.graphviz.org/download/ and download Graphviz.
Then, execute “neato -Tpng mol1_****.dot -o mol1_***.png”.
In [N1444][NTf2] example, execute “neato -Tpng mol1_C2F6NO4S2.dot -o mol1_C2F6NO4S2.png”.

Likewise, execute “neato -Tpng mol2_****.dot -o mol2_***.png”.
In [N1444][NTf2] example, execute “neato -Tpng mol1_C13H30N.dot -o mol1_C13H30N.png”.

When you execute “ls -l”, you will find two png files. After sending these png files to your local machine, open them and confirm the chemical structures.
In [N1444][NTf2] example, you will find the structure shown in Fig 1.

3-2. Handwriting the chemical structure (Recommended only if the structure is simple)
In the screen, you will find “bond matrices” shown as below. Thus, you can handwrite the chemical structure based on this information.
For example, the matrices below mean C1 is bonded to F4, F5, F6, and S1.
[[File:SDF 4.jpg]]

4. Return to the directory created in Step 1, and execute “travis HISTORY” again. Restart answering the questions. When you face “Create images of the structural formulas?”, answer no (just type Enter) this time, and keep answering until the end.
[[File:SDF 5.jpg]]

5. When you finish answering all questions, TRAVIS starts creating SDF files. W ait until ***The End*** is shown. Then, execute “ls -l”, and you will find the created files. Send SDF files(.plt) and ref file to your local machine.

Talk:Mod:Hunt Research Group/How to draw SDFs with TRAVIS

2018-03-25T11:31:57Z

Mt1817:

TRAVIS is a free tool for analyzing and visualizing trajectories from MD simulations.

TRAVIS source code can be obtained for free from "Source Code (.tar.gz)" at Download page on TRAVIS website.[http://www.travis-analyzer.de/]
How to compile and Install TRAVIS is explained on Page 3 in "Quick Start Guide (PDF)" which can be downloaded on the same link.

Details about TRAVIS is explained in the paper.[https://pubs.acs.org/doi/abs/10.1021/ci200217w]
M. Brehm and B. Kirchner. J. Chem. Inf. Model. 2011, 51 (8), pp 2007-2023.

Manual in Word format is obtained here:How to generate SDF.docx]]
*[N1444][NTf2] HISTORY(trajectory) file for trial use is here. [[Media:HISTORY.txt]]
*NB: When you use this file with TRAVIS, change the file name from HISTORY.txt to HISTORY before using. [N1444][NTf2]= tri-n-butylmethylammonium bis-(trifluoromethanesulfonyl)imide (Fig. 1)

----
'''How to draw SDFs with TRAVIS'''
*The explanation below is written to explain how to draw spatial distribution of anions in the first shell around a cation by using [N1444][NTf2] as an example.

[[File:SDF 1.jpg]]

1. Create a new directory and put HISTORY file there.
*HISTORY file is so huge that it takes much time to copy. It is recommended to make a link from the original location by executing “ln -s (Original location)/HISTORY HISTORY” in the created directory.

2. Execute “travis HISTORY” in the created directory, and answer the displayed questions based on your model (and preference). Default answers are shown in brackets and when you choose the default answers, just type Enter. Questions and answers shown below are based on [N1444][NTf2].
[[File:SDF 2.jpg]]

After answering “Create images of the structural formulas?”, press “Ctrl” and “c” at the same to quit once.
Then, execute “ls -l”, and you will find “.dot” files.
[[File:SDF 3.jpg]]

3. Visualise the “.dot” files. Choose from the options below.
3-1. Using Graphviz (Recommended)
Visit https:/www.graphviz.org/download/ and download Graphviz.
Then, execute “neato -Tpng mol1_****.dot -o mol1_***.png”.
In [N1444][NTf2] example, execute “neato -Tpng mol1_C2F6NO4S2.dot -o mol1_C2F6NO4S2.png”.
Likewise, execute “neato -Tpng mol2_****.dot -o mol2_***.png”.
In [N1444][NTf2] example, execute “neato -Tpng mol1_C13H30N.dot -o mol1_C13H30N.png”.

When you execute “ls -l”, you will find two png files. After sending these png files to your local machine, open them and confirm the chemical structures.
In [N1444][NTf2] example, you will find the structure shown in Fig 1.

3-2. Handwriting the chemical structure (Recommended only if the structure is simple)
In the screen, you will find “bond matrices” shown as below. Thus, you can handwrite the chemical structure based on this information.
For example, the matrices below mean C1 is bonded to F4, F5, F6, and S1.
[[File:SDF 4.jpg]]

4. Return to the directory created in Step 1, and execute “travis HISTORY” again. Restart answering the questions. When you face “Create images of the structural formulas?”, answer no (just type Enter) this time, and keep answering until the end.
[[File:SDF 5.jpg]]

5. When you finish answering all questions, TRAVIS starts creating SDF files. W ait until ***The End*** is shown. Then, execute “ls -l”, and you will find the created files. Send SDF files(.plt) and ref file to your local machine.

File:SDF 5.jpg

2018-03-25T11:31:20Z

Mt1817:

Talk:Mod:Hunt Research Group/How to draw SDFs with TRAVIS

2018-03-25T11:25:19Z

Mt1817:

TRAVIS is a free tool for analyzing and visualizing trajectories from MD simulations.

TRAVIS source code can be obtained for free from "Source Code (.tar.gz)" at Download page on TRAVIS website.[http://www.travis-analyzer.de/]
How to compile and Install TRAVIS is explained on Page 3 in "Quick Start Guide (PDF)" which can be downloaded on the same link.

Details about TRAVIS is explained in the paper.[https://pubs.acs.org/doi/abs/10.1021/ci200217w]
M. Brehm and B. Kirchner. J. Chem. Inf. Model. 2011, 51 (8), pp 2007-2023.

Manual in Word format is obtained here:How to generate SDF.docx]]
*[N1444][NTf2] HISTORY(trajectory) file for trial use is here. [[Media:HISTORY.txt]]
*NB: When you use this file with TRAVIS, change the file name from HISTORY.txt to HISTORY before using. [N1444][NTf2]= tri-n-butylmethylammonium bis-(trifluoromethanesulfonyl)imide (Fig. 1)

----
'''How to draw SDFs with TRAVIS'''
*The explanation below is written to explain how to draw spatial distribution of anions in the first shell around a cation by using [N1444][NTf2] as an example.

[[File:SDF 1.jpg]]

1. Create a new directory and put HISTORY file there.
*HISTORY file is so huge that it takes much time to copy. It is recommended to make a link from the original location by executing “ln -s (Original location)/HISTORY HISTORY” in the created directory.

2. Execute “travis HISTORY” in the created directory, and answer the displayed questions based on your model (and preference). Default answers are shown in brackets and when you choose the default answers, just type Enter. Questions and answers shown below are based on [N1444][NTf2].
[[File:SDF 2.jpg]]

After answering “Create images of the structural formulas?”, press “Ctrl” and “c” at the same to quit once.
Then, execute “ls -l”, and you will find “.dot” files.
[[File:SDF 3.jpg]]

3. Visualise the “.dot” files. Choose from the options below.
3-1. Using Graphviz (Recommended)
Visit https:/www.graphviz.org/download/ and download Graphviz.
Then, execute “neato -Tpng mol1_****.dot -o mol1_***.png”.
In [N1444][NTf2] example, execute “neato -Tpng mol1_C2F6NO4S2.dot -o mol1_C2F6NO4S2.png”.
Likewise, execute “neato -Tpng mol2_****.dot -o mol2_***.png”.
In [N1444][NTf2] example, execute “neato -Tpng mol1_C13H30N.dot -o mol1_C13H30N.png”.

When you execute “ls -l”, you will find two png files. After sending these png files to your local machine, open them and confirm the chemical structures.
In [N1444][NTf2] example, you will find the structure shown in Fig 1.

3-2. Handwriting the chemical structure (Recommended only if the structure is simple)
In the screen, you will find “bond matrices” shown as below. Thus, you can handwrite the chemical structure based on this information.
For example, the matrices below mean C1 is bonded to F4, F5, F6, and S1.
[[File:SDF 4.jpg]]

4. Return to the directory created in Step 1, and execute “travis HISTORY” again. Restart answering the questions. When you face “Create images of the structural formulas?”, answer no (just type Enter) this time, and keep answering until the end.

File:SDF 4.jpg

2018-03-25T11:24:01Z

Mt1817:

Talk:Mod:Hunt Research Group/How to draw SDFs with TRAVIS

2018-03-25T11:22:02Z

Mt1817:

TRAVIS is a free tool for analyzing and visualizing trajectories from MD simulations.

TRAVIS source code can be obtained for free from "Source Code (.tar.gz)" at Download page on TRAVIS website.[http://www.travis-analyzer.de/]
How to compile and Install TRAVIS is explained on Page 3 in "Quick Start Guide (PDF)" which can be downloaded on the same link.

Details about TRAVIS is explained in the paper.[https://pubs.acs.org/doi/abs/10.1021/ci200217w]
M. Brehm and B. Kirchner. J. Chem. Inf. Model. 2011, 51 (8), pp 2007-2023.

Manual in Word format is obtained here:How to generate SDF.docx]]
*[N1444][NTf2] HISTORY(trajectory) file for trial use is here. [[Media:HISTORY.txt]]
*NB: When you use this file with TRAVIS, change the file name from HISTORY.txt to HISTORY before using. [N1444][NTf2]= tri-n-butylmethylammonium bis-(trifluoromethanesulfonyl)imide (Fig. 1)

----
'''How to draw SDFs with TRAVIS'''
*The explanation below is written to explain how to draw spatial distribution of anions in the first shell around a cation by using [N1444][NTf2] as an example.

[[File:SDF 1.jpg]]

1. Create a new directory and put HISTORY file there.
*HISTORY file is so huge that it takes much time to copy. It is recommended to make a link from the original location by executing “ln -s (Original location)/HISTORY HISTORY” in the created directory.

2. Execute “travis HISTORY” in the created directory, and answer the displayed questions based on your model (and preference). Default answers are shown in brackets and when you choose the default answers, just type Enter. Questions and answers shown below are based on [N1444][NTf2].
[[File:SDF 2.jpg]]

After answering “Create images of the structural formulas?”, press “Ctrl” and “c” at the same to quit once.
Then, execute “ls -l”, and you will find “.dot” files.
[[File:SDF 3.jpg]]

3. Visualise the “.dot” files. Choose from the options below.
3-1. Using Graphviz (Recommended)
Visit https:/www.graphviz.org/download/ and download Graphviz.
Then, execute “neato -Tpng mol1_****.dot -o mol1_***.png”.
(In [N1444][NTf2] example, execute “neato -Tpng mol1_C2F6NO4S2.dot -o mol1_C2F6NO4S2.png”.)
Likewise, execute “neato -Tpng mol2_****.dot -o mol2_***.png”.
(In [N1444][NTf2] example, execute “neato -Tpng mol1_C13H30N.dot -o mol1_C13H30N.png”.)

When you execute “ls -l”, you will find two png files. After sending these png files to your local machine, open them and confirm the chemical structures.
(In [N1444][NTf2] example, you will find the structure shown in Fig 1.)

3-2. Handwriting the chemical structure (Recommended only if the structure is simple)
In the screen, you will find “bond matrices” shown as below. Thus, you can handwrite the chemical structure based on this information.
(For example, the matrices below mean C1 is bonded to F4, F5, F6, and S1.)

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File:How to generate SDF.pdf

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