[gmx-users] free energy and soft core

Berk Hess gmx3 at hotmail.com
Tue Aug 10 09:34:20 CEST 2004

>From: Frauke Meyer <fmeyer at iris3.simm.ac.cn>
>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] free energy and soft core
>Date: 10 Aug 2004 10:50:10 +0800
>Dear Berk,
>thanks for your answer.
>No matter what the structure is and if there are bad contacts, the
>free_energy              = yes
>init_lambda              = 0
>delta_lambda             = 0
>should result in an MD that does *not* depend on the soft-core
>potential, right? The reason is that the full potential is just the
>potential of topology A, since  V = (1-lambda)*V_A + lambda*V_B. And
>V_A is equal to the hard-core potential for lambda=0.
>I find a stable MD for
>sc-alpha                 = 0
>whereas mdrun crashes after 200 steps with LINCS warnings for
>sc-alpha                 = 1.5
>dG/dl is different for both, which is alright.
>                 alpha=0        alpha=1.5
>                 @TYPE xy        @TYPE xy
>                 0 173.378       0 173.378
>                 0.002 170.874   0.002 -7.056
>                 0.004 168.351   0.004 -7.9578
>                 0.006 166.028   0.006 -8.24761
>                 ....
>But should not the potential energy itself be identical for lambda=0?
>What am I doing wrong?

Are the above results with delta-lambda=0?
If delta-lambda=0 and thus lambda=0 the results should be
identical, including dvdlambda. mdrun will use the non-softcore
innerloops for lambda=0, so the results should really be identical.
But from the huge jump from t=0 to 0.002 I would guess delta-lambda
is not zero.
I just recalled that I have fixed a bug in cvs with free-energy
and rcoulomb<rvdw. But as far as I know this bug always caused
a segmentation violation.
Is rcoulomb<rvdw in your simulations?

>PS: grompp gives:
> > WARNING 2 [file fep.mdp, line unknown]:
> >   You are using lattice sum electrostatics with free energy
> >   integration.
> >   This might give wrong results, since the lattice contribution to the
> >   free energy not calculated.
>Should I better not use PME with FEP then?

The results will not be correct.
PME with free-energy will be implemented in the next release.


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