[gmx-users] Fwd: gmx select querry

shivangi nangia shivangi.nangia at gmail.com
Wed Jul 19 01:08:53 CEST 2017

Date: Mon, Jul 17, 2017 at 11:26 AM
Subject: gmx select querry
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

Hello All,

I have a question regarding the usage of gmx select.

I want to select water molecules in a particular subset in z-direction
(example z > 5 and z < 10) for each frame of my trajectory and then carry
out analysis using g_mindist on each frame of the trajectory (with

For example: system consists of peptide 1 and peptide2, membrane, water and

using g_mindist, I want to calculate the number of contacts peptide1 is
making with water vs. peptide2 in z >5 and z < 10 over the whole trajectory.

When I try to make selection using:
The option pdbatoms selected only lists the selected atoms.
The option pdbatoms all lists everything.

The -on options gives me the index file of only selected atoms:

gmx_mpi select -f 432000g1.gro -s ../../3run_npt_noposre.tpr -select
'(resname TIP3 and name OH2) and z  > -10 and z < 20'  -oi -pdbatoms
selected -on insel.ndx
I am a little confused how to incoporate the slections in odere to carry
out the analysis I am interested in.

Kindly suggest.

Thanks for your time in advance.


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