[gmx-users] problem with undistribution of water
mgoette at mpi-bpc.mpg.de
Fri Mar 7 09:22:16 CET 2008
That "problem" is called periodic boundaries.
Try inserting a second bilayer to get, at least on one axis, a water
layer between the two lipid layers, if you want to prevent PBC for a
part of the waters.
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
sudheer babu wrote:
> Thanks Mr .Justin for your response,
> I am describing answers for your questions,
> 1.My box size is 6.0nm in xyz dimensions.
> 2.The forcefield I am using "ffgmx.itp" for membrane which I downloaded
> from Pieter Tieleman webiste and deprecated FF for protein.
> 3 .I inserted protein into membrane by using genbox command.
> 4. I used force constant 10000 on protein.
> There is no leaking of membrane, the stucture is fine till EM, but in
> PR the water molecules are moving from one side of the bilyaer to the
> other side. No water mol between lipid bilyer hydrophobic region. Ok I
> tell you in clear way, Assume on membrane each side 200 water molecules
> are there but after equilabration 30 to 50 water molecules are reaching
> other side , so one side its appearing more rather than other side.
> But it looks in cubic form how appears in EM but only increasing water
> molecules on other side. Popc and protein are fine. Will it cause any
> problem later when I run further simulation by taking this output file.I
> hope you got my problem.
> Thanks in advance.
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