Talk:Mod:Hunt Research Group/ChemShell System Aqeuous Cu(II)
Creating the Fragment Input
This fragment of copper(II) and its first 2 solvation shells (18 waters in total) was taken from a DL_POLY molecular dynamics trajectory of copper(II) and 200 waters.
The following ChemShell input generates a ChemShell readable input file (cu_18water.pun) from xyz coordinates in units of Angstroms:
c_create coords=cu_18water.pun {
coordinates angstrom
cu -2.1208E+00 3.2333E+00 2.3434E+00
o -2.8625E-01 1.9061E+00 1.4529E+00
h 1.1877E-01 1.9593E+00 5.4012E-01
h -1.9888E-01 9.7326E-01 1.8024E+00
o -2.8223E+00 4.6610E+00 7.9753E-01
h -2.2564E+00 5.4307E+00 5.0188E-01
h -3.5063E+00 4.4613E+00 9.5864E-02
o -2.2571E+00 4.7205E+00 4.1738E+00
h -1.4037E+00 5.2415E+00 4.1604E+00
h -2.8973E+00 5.1460E+00 4.8133E+00
o -4.2411E+00 3.2562E+00 3.0943E+00
h -4.9570E+00 3.6912E+00 2.5482E+00
h -4.6604E+00 2.7121E+00 3.8210E+00
o -1.4300E-01 4.4480E+00 2.3166E+00
h 6.3987E-01 3.9559E+00 1.9358E+00
h 7.7886E-02 5.4206E+00 2.3892E+00
o -3.1399E+00 1.6922E+00 1.1368E+00
h -2.9742E+00 7.0608E-01 1.1396E+00
h -3.6503E+00 1.9421E+00 3.1389E-01
o -1.7364E+00 1.6708E+00 3.9303E+00
h -1.7041E+00 1.7025E+00 4.9292E+00
h -1.4097E+00 7.7998E-01 3.6143E+00
o 2.6020E+00 3.6347E+00 1.7248E+00
h 2.2869E+00 2.7841E+00 2.1456E+00
h 3.5362E+00 3.8286E+00 2.0243E+00
o -1.9034E+00 -7.5686E-01 4.9718E-01
h -2.0945E+00 -1.6870E+00 1.8370E-01
h -1.1600E+00 -3.6788E-01 -4.6901E-02
o -5.6797E+00 1.7355E+00 4.7967E+00
h -5.8293E+00 1.4817E+00 5.7523E+00
h -5.8000E+00 9.3087E-01 4.2153E+00
o -5.1385E-01 6.7028E+00 4.4103E+00
h 4.4713E-01 6.6035E+00 4.6685E+00
h -9.3334E-01 7.4261E+00 4.9588E+00
o -1.1217E+00 6.4841E+00 -2.9124E-01
h -3.5854E-01 7.0546E+00 1.2319E-02
h -9.3302E-01 6.1362E+00 -1.2096E+00
o -1.1420E+00 -8.1002E-01 3.1063E+00
h -1.7135E+00 -8.8594E-01 2.2893E+00
h -1.4996E+00 -1.4119E+00 3.8204E+00
o -6.3313E+00 4.8810E+00 1.7867E+00
h -6.4945E+00 5.6501E+00 2.4046E+00
h -6.7951E+00 5.0483E+00 9.1666E-01
o 1.3702E+00 2.5529E+00 -7.4590E-01
h 1.5559E+00 2.5872E+00 -1.7279E+00
h 2.2224E+00 2.6882E+00 -2.4052E-01
o -3.7986E+00 3.7196E+00 -1.4375E+00
h -4.4600E+00 3.0462E+00 -1.1074E+00
h -3.1624E+00 3.2791E+00 -2.0711E+00
o -5.4847E+00 1.8194E+00 -5.5093E-01
h -5.8739E+00 1.6589E+00 -1.4580E+00
h -6.1653E+00 1.5985E+00 1.4762E-01
o -2.3098E+00 2.6902E+00 6.4691E+00
h -2.9839E+00 3.4216E+00 6.5726E+00
h -1.7180E+00 2.6659E+00 7.2748E+00
}
This simple script can be directly run on the cx1 login shell. First, make sure ChemShell loaded:
module load chemshell/3.5.0
Save the ChemShell code into a file (call it cu_18water.chm) and run it using the following command:
chemsh.x cu_18water.chm
If successful, you should see a file called cu_18water.pun in your working directory. The file should containing the following:
block = fragment records = 0 block = title records = 1 molecule 1 block = coordinates records = 55 cu -4.00773230797269e+00 6.11005322112792e+00 4.42838546327008e+00 o -5.40934257429829e-01 3.60200799331702e+00 2.74558386941414e+00 h 2.24442835825121e-01 3.70254145181577e+00 1.02067916549519e+00 h -3.75828838838932e-01 1.83919537252805e+00 3.40604333831100e+00 o -5.33337556242517e+00 8.80801597862160e+00 1.50711370594938e+00 h -4.26397924354468e+00 1.02625385915255e+01 9.48416017882559e-01 h -6.62594860026623e+00 8.43063756391859e+00 1.81156756870753e-01 o -4.26530205220914e+00 8.92045471510046e+00 7.88734114815937e+00 h -2.65260931756944e+00 9.90500230678934e+00 7.86201881086833e+00 h -5.47510506218845e+00 9.72453341042410e+00 9.09582134947422e+00 o -8.01451975261362e+00 6.15332796172230e+00 5.84738121489998e+00 h -9.36737507102065e+00 6.97535906034929e+00 4.81540148395700e+00 h -8.80688214262349e+00 5.12512768410634e+00 7.22064558127293e+00 o -2.70230912881976e-01 8.40550419929390e+00 4.37774078868801e+00 h 1.20917940018035e+00 7.47556970818047e+00 3.65813287522328e+00 h 1.47183250914165e-01 1.02434523522240e+01 4.51493494445886e+00 o -5.93355275075605e+00 3.19779545999216e+00 2.14824127107853e+00 h -5.62042504261239e+00 1.33429820257137e+00 2.15353250573636e+00 h -6.89806923981172e+00 3.67003815320339e+00 5.93166302409254e-01 o -3.28132137851932e+00 3.15735530939304e+00 7.42719270559461e+00 h -3.22028320728794e+00 3.21725964462632e+00 9.31484066977507e+00 h -2.66394767755050e+00 1.47394900300478e+00 6.83003907992535e+00 o 4.91706877845385e+00 6.86858950386096e+00 3.25940054922260e+00 h 4.32161590678175e+00 5.26118800387908e+00 4.05459752922774e+00 h 6.68245142750519e+00 7.23500750391561e+00 3.82537368494394e+00 o -3.59690573132554e+00 -1.43025852254442e+00 9.39534302564061e-01 h -3.95803249672236e+00 -3.18796888134191e+00 3.47142788086846e-01 h -2.19208292967197e+00 -6.95192644972176e-01 -8.86300702452975e-02 o -1.07330805307396e+01 3.27962062452216e+00 9.06445188685995e+00 h -1.10157836396007e+01 2.80000799732324e+00 1.08702746865104e+01 h -1.09604146483599e+01 1.75908985926185e+00 7.96576480469505e+00 o -9.71036046044778e-01 1.26664598801770e+01 8.33426150407956e+00 h 8.44953483055369e-01 1.24788100224904e+01 8.82218892859793e+00 h -1.76375748412072e+00 1.40332991758940e+01 9.37077657901497e+00 o -2.11970639845953e+00 1.22531766588673e+01 -5.50363993480745e-01 h -6.77542597934990e-01 1.33312657203999e+01 2.32795427677836e-02 h -1.76315277158840e+00 1.15957407526320e+01 -2.28581337218208e+00 o -2.15806784972878e+00 -1.53071639197663e+00 5.87005793486211e+00 h -3.23804663792493e+00 -1.67418444027033e+00 4.32615125077417e+00 h -2.83383410460008e+00 -2.66810507621022e+00 7.21951174527482e+00 o -1.19644264246829e+01 9.22375584459387e+00 3.37637462969389e+00 h -1.22728298161678e+01 1.06771446214997e+01 4.54403673507691e+00 h -1.28408816512190e+01 9.53990711539915e+00 1.73223684337337e+00 o 2.58930347434184e+00 4.82428319927549e+00 -1.40954711831235e+00 h 2.94022571575571e+00 4.88910082383390e+00 -3.26525870187948e+00 h 4.19972853698533e+00 5.07996321684844e+00 -4.54517057107502e-01 o -7.17831570401030e+00 7.02902729759298e+00 -2.71648207879608e+00 h -8.42818091925602e+00 5.75648536238513e+00 -2.09268330717133e+00 h -5.97607160068503e+00 6.19660270231669e+00 -3.91381289279622e+00 o -1.03645838313550e+01 3.43816869159068e+00 -1.04110711072774e+00 h -1.11000654487933e+01 3.13486756209727e+00 -2.75522147539805e+00 h -1.16507317985402e+01 3.02072807162125e+00 2.78961450067393e-01 o -4.36489064737614e+00 5.08374267017546e+00 1.22248307589146e+01 h -5.63875539124844e+00 6.46588875186691e+00 1.24204174685879e+01 h -3.24655040791073e+00 5.03782231225216e+00 1.37473835317049e+01 block = connectivity records = 38 1 5 1 17 2 3 2 4 5 6 5 7 8 9 8 10 11 12 11 13 14 15 14 16 17 18 17 19 20 21 20 22 23 24 23 25 26 27 26 28 29 30 29 31 32 33 32 34 35 36 35 37 38 39 38 40 41 42 41 43 44 45 44 46 47 48 47 49 50 51 50 52 53 54 53 55
This .pun file can serve as input to other ChemShell calculations.