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

From: <>
Date: Mon, 15 Oct 2012 15:11:49 +0900

Thank you very much.
You were right. The nonzero elec DV/DL was due to the difference of the
box size of V0 and V1. The difference was 0.001 A. This 0.001 A difference
of box size produced 0.2 or 0.5 kcal/mol elec DV/DL.

As you pointed out, amber currently does not check the differences of box size,
while the coordinates are checked.

I expected that the final solvation free energy values change by this modification,
but I did obtain almost the same values within the precision ( < 0.1 kcal/mol difference).
The sum of elec DV/DL and vdW DV/DL by 0.001 A different box size simulations
became almost the same vdW DV/DL by the modified simulations of the exactly same box size.

Thank you very much again.
Hironori Kokubo

> >
> > 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 Sun Oct 14 2012 - 23:30:03 PDT
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