[gmx-users] Distance COM of two systems

Antonio PEÓN alopez at fc.up.pt
Wed Feb 6 17:47:55 CET 2019


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.


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