Amber Calculations on 1W7S

Full 1W7S amber input is in "though Leap into gassview" folder on the desktop

Issues with this file are:

Energy calculations

These run locally in 2 seconds and compute the energy fine - simple summation of terms

These run on CX1 using 6000MB memory and 1 processor in roughly 4 hours and 5000 steps

Attempt to run the calculation on 2 processors witht 7000MB memory - time should be halfed but CPU time remains around 4 hours.

Issues with the optimisation:

Not a smooth start to the energy profile - jump from -2 to 200 kJ/mol! - this smooths out

VMD allows overlay of the 2 structures (start and finish) so we can see whats moved
It also has a RMS fit to calculate some "fit factor"
Can also print out a distance matrix using 3rd party script in VMD tcl console. This creates a full matrix/surface.
I and Mike wrote scripts to pull the diagonal out of the file so we are comparing each residue with itself.
This plots the classic movement per residue - BASED ON CENTER OF MASS.

The optimised file can be submitted for a frequency calculation using only Amber. Questions to answer about this are:

Do H and L ONIOM tags get interpreted for Amber only calculations (giving % frequency in the diff regions)?
Can this calculation be run in parallel NProc=2?
Does the Chk file load in Gaussview? How large is it?

The initial frequency calculation ran successfully but created a 1.6Gb text file which made reading it difficult.

Answer to the ONIOM tag question:

It seems Gaussian does recognize the ONIOM split in pure frequency calculations even if no ONIOM method is being used.