Re: [gmx-users] problem with undistribution of water

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 & comp

Re: [gmx-users] problem with undistribution of water

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 prot

[gmx-users] problem with undistribution of water

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 usi

Re: [gmx-users] problem with undistribution of water

Quoting sudheer babu <[EMAIL PROTECTED]>: > 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

[gmx-users] problem with undistribution of water

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 due