Re: [AMBER] the origin of ELEC DV/DL in the case of softcore TIcalculation of the solute with no charge by crgmask

From: David A Case <>
Date: Thu, 11 Oct 2012 10:45:40 -0400

On Fri, Oct 05, 2012, wrote:
> Attached are the input files for lambda=0.50 for step2w (vdW softcore
> with no charge solute by scmask).

You left out the minimization inputs, but I was able to figure out what is
going on:

The box dimensions for the wat.crd and ala2wat.crd files are different.
This means that all components of the energy of the two systems will differ,
including changes in electrostatic energies. If you change the coordinate
file to have the same box dimensions, the EELEC component of DV/DL is zero, as
it should be.

(Also, the water coordinates are different in the two files, but sander tries
to compensate for this. It doesn't seem to check the box sizes in the two
prmtop files.)
> It will take some hours by 8 cpu cores, but if you decrease the total
> timestep to 0.1 ns or something, it will finish soon.

Finishes even more quickly if, as I did, you change nstlim to 10 and ntpr to
1. When you are searching for problems, don't run a calculation that takes
hours to complete!

...good luck....dac

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Received on Thu Oct 11 2012 - 08:00:10 PDT
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