[gmx-users] FEP softcore problematics

Maik Goette mgoette at mpi-bpc.mpg.de
Wed Jun 21 17:38:47 CEST 2006

Thank you Berk and David

I'll try the ways you suggested.


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

Berk Hess wrote:
>> 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.
> Berk.
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