[gmx-users] RE: Problem with setting vsite=aromatics on OPLSAA

Berk Hess gmx3 at hotmail.com
Tue Nov 4 16:19:55 CET 2008


Did you read my previous mail?

Indeed mdrun does not work for vsite aromatics in Gromacs 4.0.
These were some other mails on that topic this day.
I think you were (un)lucky that grompp did work in Gromacs 3.3.

As I said, I would not use vsite aromatics.
Simply use vsite hydrogens and a time step of 5 fs.


> From: genesup at gmail.com
> To: gmx-users at gromacs.org
> Date: Tue, 4 Nov 2008 18:11:23 +0300
> Subject: [gmx-users] RE:    Problem with setting vsite=aromatics on OPLSAA
> OK,
> I`ve switched from version 3.3.3 to 4.0 and now I do not have a
> segmentation fault when setting -vsite aromatics with OPLSAA.
> Instead when I build trp and execute mdrun it trews the following error:
> ------------------------------------------------------------------------
> Program mdrun, VERSION 4.0
> Source code file: vsite.c, line: 1504
> Fatal error:
> Virtual site atom 133 is part of a charge group of only virtual sites,
> but its first constructing atom (139) is part of a different charge
> group, this combination is not allowed
> ------------------------------------------------------------------------
> Any suggestions on how to make it work?
> Thank you.
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