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

ABEL Stephane Stephane.ABEL at cea.fr
Thu May 16 11:44:05 CEST 2019

Thanks Justin

but it does not work either

LIPIDC is indeed in a group (#27)  

So I when typed with GMX5.1.4 or GMX2018.2

LIPIDC & a C31 | a C32 | a C33  ---> Syntax error: "LIPIDC & a C31 | a C32 | a C33" 
27 & a C31 | a C32 | a C33  ---> the command works  but I selected "all" the C31, C32 and C33 atoms and not only those in the LIPIDC group


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
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


More information about the gromacs.org_gmx-users mailing list