[gmx-users] after simulation coulombic and van der waals energies shows zero -protein-ligand simulation

Justin Lemkul jalemkul at vt.edu
Wed Dec 9 16:35:41 CET 2015

On 12/9/15 7:33 AM, Nikhil Maroli wrote:
> Dear gromacs users
> im running protein-ligand simulations by following the tutorial
> i completed the simulation rmsd values are fine
> at zero time hydrogen bond was one and at 100ns also one in between it was
> from 1 to 6(varying)
> now when i try to plot coulombic and van der vaals interactions for 1-100ns
> it is zero and when i load trajectory in vmd there is no movement even for
> water molecules.

Did you do the run on a GPU?  If so, energygrps don't work.  Use mdrun -rerun to 
calculate interaction energies on CPU.

The molecules not moving is inconsistent with your above statements regarding 
RMSD and variations in hydrogen bonds.  If nothing moved, your RMSD would always 
be zero and the number of hydrogen bonds would not change.  You're probably 
loading the trajectory incorrectly.



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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