Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI

From: David A. Case <>
Date: Mon, 2 Jul 2007 23:34:13 -0700

On Mon, Jul 02, 2007, Holly Freedman wrote:

> Does anyone know an easy way to compare the perturbed and unperturbed force
> fields?

Take a restart file (or other coordinates) and just run a single step of
minimization. Do this once with clambda=0.0, and once with clambda = 1.0.
You should see differences in just whatever has changed (e.g. the vdW terms,
if that is all you are changing.

You can also use "diff" on the two prmtop files (I'm assuming amber9 here).
You'll have to look at the file formats to interpret the results, and there
might be some noise caused by irrelevant differences, but this could help.
One "expert" way to check this is to create prmtop.1 file by editing the
prmtop.0 one, and changing just the parts you want changed. It's not really
brain surgery, but does require and understanding of the innards of prmtop

Note: depending on the environment of the atoms that are being changed, it is
certainly possible that nothing is wrong, and that there are indeed large
flucutations in dV/dl. But poking around some to be sure that there are no
other problems is certainly warranted.

...good luck.....dac

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Received on Wed Jul 04 2007 - 06:07:28 PDT
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