----- Original Message ----- From: priyanka srivastava <priyanka...@yahoo.com> Date: Saturday, January 31, 2009 10:20 pm Subject: [gmx-users] COM motion removal To: gmx-users@gromacs.org
> 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. If your peptide atoms can see both sides of the bilayer, then your lipid headgroups can also see their counterparts and you are not simulating a bilayer. I am not sure what you think your issue is... you say the peptide "came very close to the edge" and then "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. As Justin said, you should consult the other possibilities trjconv permits and be prepared to try a few iterates with different options to see what they do. You can't force the "environment of the peptide" to remain the same - you are sampling from a heterogenous simulation environment. If it moved from the centre of the bilayer then postprocessing won't move it back. > 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? PBC will be taken care of. You can verify this by counting a single example (approximately) by hand. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
