[gmx-users] Question

Justin Lemkul jalemkul at vt.edu
Wed Aug 12 22:24:01 CEST 2015

On 8/12/15 3:47 PM, Eric Smoll wrote:
> Hello gromacs users,
> I am running a set of MD simulations where we are only interested in
> logging the coordinates and kinetic energy of a specific group in the
> system. I want to write the coordinates and energy of this group to file at
> every timestep.
> Supplying an index file with the group of interest to grompp and specifying
> this group in the mdp file under "energygrps" doesn't seem to impact the
> edr file. The edr file still outputs the total system energy as a function
> of time. Is there someway I can request that gromacs only compute the
> energy of one group in my system? Will this result in a speedup?

energygrps only decompose the short-range nonbonded interactions, nothing else.

> Are there other ways I can increase the speed of my simulation? My systems
> have 20,000-40,000 atoms with PME and 1.5 nm cutoffs. Are these simulations
> well suited for GPU acceleration or is this unlikely to produce a speedup?

Depends on a lot of factors, but probably.  That's a rather small system.

Otherwise, if you just want to get the KE of some group, either:

1. Use gmx traj to calculate it from the velocities in the .trr (remember to 
account for any constraints that may be in use)

2. Extract the relevant group(s) of atoms from the .tpr and .trr (gmx 
convert-tpr and gmx trjconv, respectively) and use mdrun -rerun on the .trr



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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