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

Justin Lemkul jalemkul at vt.edu
Tue Mar 1 19:22:08 CET 2016

On 3/1/16 4:27 AM, Nikhil Maroli wrote:
> 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?

If you want nonbonded interaction energies, you need to set appropriate 
energygrps in the .mdp file.  Generate a new .tpr with the desired groups and 
recalculate the energies with mdrun -rerun on the existing trajectory.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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