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
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.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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