[gmx-users] position restraints
dmobley at gmail.com
Thu May 11 20:37:21 CEST 2006
OK, I am running MD using position restraints, and I don't get a
separate energy output for "restraint energy" or some such; as far as
I can tell the energy of the restraints is grouped in with the total
potential energy and never reported separately. I would like it to be
reported separately, as well (perhaps in the .ene file). Is there a
way I can get this?
On 5/11/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> David Mobley wrote:
> > Dear all,
> > I'm trying to figure out if there is currently a way to calculate the
> > position restraint energy (for example, if I'm using a posre.itp file
> > to harmonically restrain some atoms) on the fly. Can anyone give me
> > some pointers? I haven't turned up anything useful on this since 2001
> > on the mailing list.
> > In particular, I would *very much* like to be able to somehow get the
> > position restraint energy without having to save trajectory snapshots
> > and reprocess the trajectory somehow, as I need to get the position
> > restraint energy every 0.2 ps or so over fairly long trajectories, and
> > I would rather not have to save trajectory snapshots this often to
> > disk.
> > Will I have to modify the code to get this, or is there something more
> > straightforward I can do?
> It's not entirely clear to me what you want. If you apply position
> restraints you get the energy.
> Where's the problem?
> > Thanks,
> > David
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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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