[gmx-users] Removing PBC from Replica Exchange Trajectory

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Mar 14 20:18:46 CET 2007

Hi Bob,

You could try -pbc cluster. If that doesn't work, it'll be difficult.
The option -pbc nojump will only work on continuous trajectories.



On 3/14/07, Robert Johnson <bobjohnson1981 at gmail.com> wrote:
> Hello everyone,
> I'm trying to visualze the conformations of a ssDNA molecule obtained from a
> REMD trajectory. As expected, there are parts of the simulation where the
> oligomer is broken due to the PBC wrapping. I've been trying to fix this with
> trjconv. However, the -pbc nojump option doesn't work - it actually makes the
> broken portions of the molecule worse and gives a terribly distorted
> trajectory. Since the REMD trajectory isn't continuous (i.e. there are
> instaneous jumps in the coordinates associated with REMD swaps), the nojump
> option may have problems. Does anyone know of any other way or other tools that
> I could use to reassemble my broken DNA strand?
> Thanks,
> Bob Johnson
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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