[gmx-users] Strange dgdl-value together with lincs
gmx3 at hotmail.com
Tue Feb 19 13:52:27 CET 2008
> From: gmx3 at hotmail.com
> To: gmx-users at gromacs.org
> Subject: RE: [gmx-users] Strange dgdl-value together with lincs
> Date: Tue, 19 Feb 2008 11:20:14 +0100
> > Date: Fri, 15 Feb 2008 09:27:24 +0100
> > From: mgoette at mpi-bpc.mpg.de
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Strange dgdl-value together with lincs
> > Berk,
> > here comes the topology for this run (vdw morph):
> > Its OPLSAA and the hydrogens have bond terms. This is the standard
> > OPLSAA FF for ethane and methanol.
> > Thanks.
> OK, I found the problem.
> You have a delta_lambda of 0.02, which is so high that the kinetic energy
> of the constrained degrees of freedom is no longer negligible.
> I am not sure if constraints with kinetic energy are formally correct.
> But anyhow, you had unconstrained_start=yes, which is probably incorrect,
> since I assume your equilibration run had delta_lambda=0 and therefore
> in the starting configuration the constraint velocity is zero.
> The spike in dG/dl therefore corresponds to building up this kinetic energy.
> Now even if you would set unconstrained_start=no, this would not help,
> since Gromacs would not put velocities into the constraints at startup.
> I have managed to fix this in the code (not committed).
> But when delta_lamda is so large, the is another issue.
> The coordinates are constrained after the update with lambda of the current
> step, but the constraints in the updated configuration should actually obey
> the lengths for the next step.
> I have to think if things can still be somewhat correct with such a large delta_lambda,
> before I starting correcting these two issues.
I have now properly fixed this issue in the CVS head branch.
The constraint lengths are now exactly correct at every step
and with unconstrained_start=no the spike in dG/dl due to the velocity is gone.
Note that the error would normally be extreme small, since delta_lambda
is normally extremely small.
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