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

van Bemmelen J.J.M.vanBemmelen at student.TUDelft.NL
Wed Feb 20 08:14:09 CET 2008


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.


>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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