[gmx-users] COM motion removal

priyanka srivastava priyankaps4 at yahoo.com
Sat Jan 31 12:13:03 CET 2009

Dear Gromacs users!!

I have a lipid - peptide system which I simulated for 50ns. Now in the beginning of the simulation the peptide was at the center of the bilayer but with time the peptide moved and came very close to the edge. Now near the edge it is having the interactions with the images of the lipid bilayer, since pbc is on, but when I view it using ngmx then the peptide appears to be lying near the edge. 

Is there any way by which I can write the coordinates of the images of the lipid bilayer since pbc is on?Using trjconv is not helping me since it moves the entire system i.e.
lipid bilayer+water+peptide. So what I am looking for is an option to
get the images atoms so that the environment of the peptide remains
same and at the same time the peptide is positioned near the center of the box. 

Also I carried out an analysis in which I calculated number of water molecules around residue 1 which is actually lying very close to the edge (rather outside). I think if the pbc is on then the images are taken care of automatically and it will already construct image boxes around those residues which are close to the edge and then perform the number of water molecules around residue 1 calculation?

Eagerly waiting for your responses,

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