[gmx-users] problem with undistribution of water

sudheer babu sudheer.pbm07 at gmail.com
Fri Mar 7 06:23:19 CET 2008

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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