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

Maik Goette mgoette at mpi-bpc.mpg.de
Wed Feb 20 09:38:55 CET 2008


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.


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/

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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