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.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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