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

[Berk Hess]

No, I meant just the 1+3 plots of  as a function of lambda.

Berk.

> Date: Wed, 20 Feb 2008 09:38:55 +0100
> From: mgoette at mpi-bpc.mpg.de
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Strange dgdl-value together with lincs
> 
> Jeroen,
> 
> I'm aware of that bug and using the 3.3.2_pre, with the bugfix included.
> Btw, I don't see how to sample "backwards" ;)
> Probably you mean in the case of slow growth, no?
> In that case, the problem occurs in both directions.
> 
> Berk, there are quite a few files (44 in that case).
> I will sample the system a bit longer (66ns for each case in total) and 
> make a gz-download.
> Anyway, to me they look normal.
> 
> Regards
> 
> Maik Goette, Dipl. Biol.
> Max Planck Institute for Biophysical Chemistry
> Theoretical & computational biophysics department
> Am Fassberg 11
> 37077 Goettingen
> Germany
> Tel.  : ++49 551 201 2310
> Fax   : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
>          mgoette2[at]gwdg.de
> WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/
> 
> 
> van Bemmelen wrote:
> > Maik,
> > 
> > This is just a hunch, but since you're turning charges on (instead of
> > off) in the third step, maybe this is also a case of bug 175
> > (http://bugzilla.gromacs.org/show_bug.cgi?id=175). That is, if you're
> > using PME for electrostatics.
> > 
> > This bug has been fixed for the CVS version. Another "fix" would be to
> > do all steps in the reverse direction.
> > 
> > Greetz,
> > Jeroen
> > 
> > 
> >> 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.
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