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
Hi gmx users,
I inserted my protein into Popc Bilayer . EM is fine, when I do
equilibration the water molecules from oneside of bilayer moving to other
side, it looks undistribution of water , but total sturucture in cubic form.
can you give me detailed information regarding this problem
is it
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
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
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