[gmx-users] COM motion removal

[Justin A. Lemkul]

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.

-Justin

> Eagerly waiting for your responses,
> Priyanka.
> 
> 
> 
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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