[gmx-users] Measuring dihedral energy of various selections
David van der Spoel
spoel at xray.bmc.uu.se
Fri Aug 18 15:05:33 CEST 2006
Berk Hess wrote:
>> From: Erik Marklund <erikm at xray.bmc.uu.se>
>> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Subject: Re: [gmx-users] Measuring dihedral energy of various selections
>> Date: Fri, 18 Aug 2006 14:05:18 +0200
>> Just from the top of my head, couldn't you just make a new mdp- and a
>> tpr-file with different energy groups and then use mdrun -rerun on the
>> old trajectory?
> No, energy groups only work for non-bonded interactions.
> You could remove or comment out all the dihedrals in the topology
> that you do not want and then do mdrun -rerun
you may also need to check the 1-4 interactions, depending on the
problem which you did not mention.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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