[gmx-users] Trajectory visualization and PBC
spoel at xray.bmc.uu.se
Mon Aug 8 21:40:29 CEST 2005
On Mon, 2005-08-08 at 16:13 -0300, Monique Brito wrote:
> > Hi, people,
> > We're doing our simulation of a 953 residue
> > protein in vacuo.
> > After energy minimization we run 3 ns of
> > dynamics.
> > When we visualize the trajectory without
> > removing PBC, we
> > don't see anything abnormal, but when we remove
> > PBC, with trjconv, the structure shows a
> > deformed and strange
> > trajectory, with several strechted bonds, as if
> > some chais were entirely moved
> > away from the rest of the body of the protein.
> > But the plot of the potential energy vs.
> > trajectory shows nothing wrong.
> > Is it necessary to remove PBC to see the real
> > trajectory or can we see it with PBC? Is it the
> > same result?
What's the point of PBC in vacuo? You typically want a protein in an
infinite box (pbc=no) with center of mass motion removal mode set to
> > Thanks,
> > Monique Brito
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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://xray.bmc.uu.se/~spoel
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