[gmx-users] rerun under non-bonded E. terms

Justin Lemkul jalemkul at vt.edu
Tue May 12 13:59:56 CEST 2015

On 5/12/15 7:57 AM, Albert Solernou wrote:
> Thanks Justin,
> still I would not know how to go from a .edr file into a trajectory that has the
> forces of the atoms I am interested in.

You don't.  The .edr file is the energy output of a simulation.  If you have 
your subtrajectory of interest, you'll get a new .edr file with the quantities 
you want, if I understand your description.


> Best,
> Albert
> On 05/12/2015 12:48 PM, Justin Lemkul wrote:
>> On 5/12/15 7:46 AM, Albert Solernou wrote:
>>> Well, back to the beginning, then.
>>> Is there a way to do a re-run using only non-bonded energy terms? I'll explain a
>>> bit further. I have a trajectory, and want to get a (sub)trajectory that has
>>> only a sub-set of atoms and that accounts only for the non-bonded interactions
>>> within this sub-set of atoms. So far, I have the extracted temporary
>>> sub-trajectory that contains the solvent atoms as well as the residues I am
>>> interested in. Is there an easy way to do that? Or should I modify the source
>>> code, instead?
>> The nonbonded terms don't depend on the bonded terms; they are, by default,
>> saved in the .edr file.  If you want some group-wise decomposition (e.g.
>> interaction energy) then that's what energygrps are for.  There is no need to
>> modify code or hack the topology at all if this is what you're after.
>> -Justin


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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