[gmx-users] COM motion removal

Mark Abraham mark.abraham at anu.edu.au
Sun Feb 1 12:59:14 CET 2009

----- Original Message -----
From: priyanka srivastava <priyankaps4 at yahoo.com>
Date: Saturday, January 31, 2009 10:20 pm
Subject: [gmx-users] COM motion removal
To: gmx-users at 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.


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