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