[gmx-users] index file after MD for non bonded interactions

Nikhil Maroli scinikhil at gmail.com
Tue Mar 1 10:27:44 CET 2016

Dear all,
i have generated cyclic peptide nanotube in Lipid bilayer system and input
files for GROMACS  from charmm-gui . 50 ns MD is performed and i  would
like to  study non bonded interactions, when i invoke gmx energy- i got 50
options ,but none of them contain option such as
Protein-Membrane,membrane-water,protein-water or the ring1-ring2 etc.when i
checked in index file i have seen only three groups such as
PROT,MEM,SOL_ION,in order to get  Interactions between the membrane protein
and the each ring (options that i wanted ) ,if i create an index file it
will work? as i understood -n index option not available with gmx energy
command,should i make my index files first before doing MD? or is there any
option that i can do for energy now, with the 50ns MD results?

Nikhil Maroli

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