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

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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