[gmx-users] Fwd: -pbc nojump

Carsten Kutzner ckutzne at gwdg.de
Wed Oct 27 09:51:28 CEST 2010


with the nojump option, your water molecules will slowly
diffuse out of the "home" box and appear far away from your
protein if you display the MD system with VMD or pymol.

You can split your trajectory in two parts (using index groups)
and use different options on them individually:
a) on the water part (and also on the ions, if they are present),
   use trjconv -pbc mol
b) on the rest, use trjconv -pbc nojump

Then overlay both results in the visualization program.


On Oct 27, 2010, at 9:40 AM, David van der Spoel wrote:

> I did simulation of protein-dna complex in water solvent. After
> simulation, two strands of dna was separated when I displayed my a.xtc
> with VMD.I used (trjconv –f a.xtc –s a.tpr –n a.ndx –o b.xtc –pbc
> nojump) and problem fixed. But now I have another problem. Before using
> –pbc nojump, there were water molecules in interface of between protein
> and dna but, After using of –pbc nojump, 1) there was no water molecule
> in interface of between protein and dna. 2) The distance between water
> molecules and protein or dna was increased.
> I want to survey interfacial water molecules and dynamics of water
> medited hydrogen bonds.
> I had sent my question to gromacs mailing list, before, but my problem
> was not solved.
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Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302

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