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

Shweta Kumari shwetaasingh7 at gmail.com
Mon Feb 18 17:40:36 CET 2019

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!

Best Regards,

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