[gmx-users] Distance COM of two systems

[Justin Lemkul]

On 2/6/19 11:26 AM, Antonio PEÓN wrote:
> Hello,
> I would like to calculate the distance from the center of masses (COM) 
> between two systems. One would be the center of mass of waters and
> another would be the center of mass of a lipid membrane. I was using
> this command and wanted to know if it is correct.
>
> gmx pairdist -f total.xtc -s md_0143.tpr -n in13.ndx -sel 2 -ref 5 -o
> distpair.avg -selrpos whole_mol_com -seltype whole_mol_com
> where 2 and 5 are the lipid membrane and waters respectively.
> Thanks in advance.
>

You want gmx distance -select "com of group 'X' plus com of group 'Y'" 
substituting in real group names for X and Y.

-Justin

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Justin A. Lemkul, Ph.D.
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