[gmx-users] select an atom for "only" residue with make_ndx

Justin Lemkul jalemkul at vt.edu
Wed May 15 18:13:57 CEST 2019

On 5/15/19 11:03 AM, ABEL Stephane wrote:
> Hello all,
> I am currently doing simulations of a model of membranes with different types of lipids (LIPIDA, LIPIDB and LIPIDC)  and I would like to select a group of  atoms for only the same lipid with make_ndx. Below an example
> Three different lipids : LIPIDA, LIPIDB and LIPIDC contain few atoms with the same name (C31, C32 and C33). With make_ndx I would like to have the atoms C33 and C32 for "only" the LIPIDC
> So If I do
> rLIPIDC & aC32 | aC33 ---> I have the indices of the C32 and C33 of the 3 lipid types.
> So what is the exact command

Each different [moleculetype] already has its own default group, so 
choosing atoms in LIPIDC should be as simple as:

N & a C31 | a C32 | a C33

where N is the group corresponding to LIPIDC.



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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