Thank you Berk and David
I'll try the ways you suggested.
regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Berk Hess wrote:
From: Maik Goette <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
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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