[gmx-users] Strange dgdl-value together with lincs

Berk Hess gmx3 at hotmail.com
Tue Feb 19 11:20:14 CET 2008

> 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.


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