[gmx-users] free energy and soft core
fmeyer at iris3.simm.ac.cn
Tue Aug 10 04:50:10 CEST 2004
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.
@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?
PS: grompp gives:
> WARNING 2 [file fep.mdp, line unknown]:
> You are using lattice sum electrostatics with free energy
> This might give wrong results, since the lattice contribution to the
> free energy not calculated.
Should I better not use PME with FEP then?
On Mon, 2004-08-09 at 16:08, Berk Hess wrote:
> >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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