[gmx-users] FEP softcore problematics

Berk Hess gmx3 at hotmail.com
Wed Jun 21 15:49:36 CEST 2006

>From: Maik Goette <mgoette at mpi-bpc.mpg.de>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] FEP softcore problematics
>Date: Wed, 21 Jun 2006 14:55:34 +0200
>Hi David
>Thank you for the detailed answer.
>It sounds reasonable. :)
>For sure it's the best way to make the calculations separatly and sum up 
>the energies at the end. You mentioned, that, in the case of splitting, the 
>"density" of snapshot samplings at lambda=0,1 can be lower.
>So I guess, one reaches approx. 30-35 samplings, when splitting the terms. 
>In the first place, this is no big deal, because of the possibility of 
>parallelization, but for screening purposes in the future, the amount of 
>simulation time in total is quite critical for me.
>I tried to find that paper, but unfortunately didn't.
>It would be great, if you could give me some more info about it, cause I 
>would like to have a look into it, at least.

I assume you want to mutate some atoms into other types of atoms.
Then the procedure has to be done in three steps:
1) make the charges of the atoms present in the A-state go to
those of the B-state
2) change the LJ of the A-state to the B-state.
3) make the charges of the atoms present in the B-state go to
those of the B-state.

Steps 1) and 3) will be computionally very cheap as linear
electrostatics interpolation without soft-core is very smooth
so you need very few lambda points.
Step 2) can be done with sc_power=1

This procedure will be more efficient than any single-step
procedure that Gromacs supports.

I had implemented the same soft-core dependence for Coulomb
and LJ in Gromacs because a different soft-coring of Coulomb
and LJ might result in additional minima in the energy landscape
for intermediate lambda values, this can complicate the sampling.


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