[gmx-users] free energy and soft core
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
>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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