[gmx-users] Doubt about edr file after normal mode analysis

Justin Lemkul jalemkul at vt.edu
Fri Jul 21 23:14:56 CEST 2017

On 7/21/17 4:24 PM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
> I attempted to write the energy file (edr file) after performing normal mode analysis (using integrator = nm), but couldn't find gromacs writing nm.edr file at the end of the nm analysis similar to the way it writes em.edr after energy minimization. So firstly, is it plausible to write the edr file after nm analysis and if it is, what correction should I implement in the following set of gromacs commands I executed, to pull it off?
> grompp_d -f nmnopbc.mdp -c em.gro -p topol.top -o nm.tpr
> mdrun_d -v -deffnm nm -e nm.edr

I don't think there is any physically meaningful energy quantity one can get 
from NMA, hence no .edr file.



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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