[gmx-users] free energy and soft core

Berk Hess gmx3 at hotmail.com
Mon Aug 9 10:08:51 CEST 2004

>From: Frauke Meyer <fmeyer at iris3.simm.ac.cn>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] free energy and soft core
>Date: 06 Aug 2004 10:57:52 +0800
>Hi all,
>for the perturbation of a ligand (A) to dummy atoms (B) I want to use
>soft core potential. With
>free_energy              = yes
>init_lambda              = 0
>delta_lambda             = 0.000001
>sc-alpha                 = 1.5
>sc-sigma                 = 0.3
>I get LINCS warnings after the first few steps and mdrun crashes,
>sc-alpha                 = 0
>sc-sigma                 = 0.3
>the whole perturbation runs fine (though with the expected singularities
>for lambda near to 1).
>Surprisingly, with larger sc-alpha (eg. 10) LINCS warnings are fewer and
>stop after some steps, and the perturbation terminates normally.
>What might the problem here be? Topology B (dummies covalently boudn to
>each other) anyway has no dispersion. I expected less warnings and
>results to alpha=0 with *lowering* alpha, but did not find that.
>Another surprise was that the dynamics depend on sc-sigma: Higher
>has the same effects a higher sc-alpha. But should not sigma_A be
>calculated brom C6_A and C12_A, and sigma_B not play a role, because
>C6_B = C12_B = 0 anyway, so that sc-alpha is not used for the distortion
>of LJ?

This is correct.
But sc-alpha is also used for particles that only have charge and no LJ
interactions. Could it be that you have such kind of atoms in your such,
for instance hydrogens?

It is not surprising that with a larger sc-alpha everything goes fine.
A larger sc-alpha makes a larger soft core and thus the whole
potential gets smoother.

But the difference between 0 and 1.5 is quite strange.
Also a few steps into the simulation lambda should be almost 0
(or am I wrong?) and thus there should be almost no soft-core
effect present yet. Therefore I would expect the same behavior
independent of the sc-alpha value.

The problem could just be a bad starting structure, too close
atoms contacts or something like that.


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