[gmx-users] COM motion removal

Justin A. Lemkul jalemkul at vt.edu
Sat Jan 31 13:44:03 CET 2009

priyanka srivastava wrote:
> 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.

Saying that "trjconv is not helping" is not useful, because indeed trjconv is 
capable of doing exactly what you want.  Sometimes it may take several 
iterations using different options for -pbc, -center, etc.  I have found that 
for systems like this using trjconv -center (and then choosing Protein as the 
group to be centered) does the trick nicely.

> 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?

Try getting the protein centered (as I've described above) and compare your 
results with the non-centered structures.  I believe most, if not all, Gromacs 
tools take periodicity into account by default.


> Eagerly waiting for your responses,
> Priyanka.
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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