[gmx-users] PBC and large hydrogen-bonded molecules
tsjerkw at gmail.com
Tue May 23 10:52:48 CEST 2006
On 5/23/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> mernst at tricity.wsu.edu wrote:
> > Hello fellow Gromacs-users,
> > Today I was extracting PDB snapshots from a solvated DNA 12mer
> simulation trajectory.
> > When I went to view the snapshots, I saw that one of the DNA strands
> suddenly jumped
> > some nanometers away from its partner during certain frames. I
> remembered that there was
> > a note about fixing this artifact in the trjconv documentation, and soon
> found that the
> > -whole or -nojump options produced an easier-to-view snapshot series.
> Well done.
Hear, hear! :)
> The simplest hypothesis for these images is that the visualisation
> program is placing the first atom it finds in each molecule inside the
> box and the rest of it consistent with that placement. More visually
> appealing might be an algorithm that located the center-of-mass
> inside... shrug. Playing with the trjconv options before the
> visualisation program gets into the mix may help here.
In fact, it is Gromacs which uses the first atom to decide in which box the
molecule should be located during MD. But ALWAYS think of the simulation
system as an infinite tiling of simulation unit cells. It doesn't matter a
bit how you choose your single simulation cell from that infinite system..,
except for visualization.
Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
9747AG Groningen, The Netherlands
+31 50 363 4336
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