[gmx-users] How to replacing molecule outside the 2.5nm cutoff distance from protein surface in gromacs?

Justin Lemkul jalemkul at vt.edu
Sun Feb 24 00:49:09 CET 2019

On 2/18/19 11:39 AM, Shweta Kumari wrote:
> Dear gromacs users,
> I have protein-membrane (POPC only) system. I want to replace the
> cholesterol molecules with POPC but outside a 2.5nm cutoff distance of
> protein surface.
> I am using this command :
> gmx insert-molecules -f system.gro -ci cholesterol.pdb -nmol 10 -try 10
> -replace POPC -o output.pdb
> But this command randomly select the POPC molecules and replace it with
> cholesterol. In this way few cholesterol molecules are coming near the
> protein (within 2nm).
> Thanks in advance!

Use gmx select to create an index group of POPC molecules that satisfy 
the geometric criterion, and use that as your replacement group.



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


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