[gmx-users] Strange dgdl-value together with lincs
gmx3 at hotmail.com
Tue Feb 19 16:21:16 CET 2008
There could be many problems at different points.
One can't say much without having looked in detail at all the data.
Methanol will strongly hydrogen bond to water. So you need to be very careful
that you sample the process of (dis)appearing this hydrogen bond carefully,
both in the 1 and 3 step process. But the "path" could be quite different
in the 1 and 3 step process. So you have to choose your alpha, sigma
and lambda points carefully.
Maybe you could post links to dG/dlambda plots for the 1+3 parts?
> Date: Tue, 19 Feb 2008 16:07:50 +0100
> From: mgoette at mpi-bpc.mpg.de
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Strange dgdl-value together with lincs
> Thanks, Berk
> I'm also quite sure, that this spike doesn't explain the deviations I
> see in adding up single DG contributions. Maybe I just bring it up once
> Assume, you take the interconversion of ethane to methanol in solvent in
> one step.
> You sample hardcore at 11 evenly spaced lambda values for, lets say, 2
> ns each.
> You get the dG/dl mean from every run and integrate via simpson to get a
> total DG.
> Now, you do the same, but split your process into 3. Switching charges
> to zero, morph the vdw and bondeds, switching charges back on. All
> hardcore to keep comparability.
> You take 3x11 lambda snapshots and sample for 666ps each.
> You do the integration 3 times like above.
> The sum of these 3 DGs should yield the same DG as the run above, I suppose.
> Unluckily, both numbers deviate by roughly 10 kJ. I have the feeling,
> that hydrogen bonding could play a role, but intuitively, I'd say it
> shouldn't differ in the free energy of both.
> Thanks again for the help
> Maik Goette, Dipl. Biol.
> Max Planck Institute for Biophysical Chemistry
> Theoretical & computational biophysics department
> Am Fassberg 11
> 37077 Goettingen
> Tel. : ++49 551 201 2310
> Fax : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
> WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
> Berk Hess wrote:
> > ----------------------------------------
> >> 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.
> >> Berk.
> > 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.
> > Berk.
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