[gmx-users] Fwd: -pbc nojump

David van der Spoel spoel at xray.bmc.uu.se
Wed Oct 27 09:51:18 CEST 2010

On 2010-10-27 09.40, 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.

try using some of the suggestions that have been posted.
e.g. trjorder springs to mind.

also if you make claims like "The distance between water
 > molecules and protein or dna was increased." you should provide 
evidence. Either the statement does not say what you mean or you have 
not measured correctly (e.g. g_mindist).

> I had sent my question to gromacs mailing list, before, but my problem
> was not solved.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

More information about the gromacs.org_gmx-users mailing list