[gmx-users] Regarding g_enemat

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 13 21:06:26 CEST 2011

bipin singh wrote:
> Hello,
> I am using g_enemat to calculate the energy matrix from the energy
> file(edr file) and I am supplying Protein as a group in -groups
> option.
> The command I am supplied is as follows:
> g_enemat -f file.edr -groups groups.dat -emat emat.xpm -etot
> energy.xvg -temp 328 -nocoul -nolj -nomean
> but I am getting the following error
> Read 1 groups
> group 0WARNING! could not find group (null):Protein-Protein (0,0)in energy file
> As written in the manual:
> "Energy groups with names like ’Coul-SR:Protein-SOL’ and
> ’LJ:Protein-SOL’ are expected in the energy
> file"
> But I am not clear how to get these terms in energy file.....

Whatever name you supply has to be an actual term in the .edr file.  Run 
g_energy first to get a list of all valid energy terms if you are unfamiliar 
with the contents of the .edr file.


> The energy file I am supplying is from a 100 ns md simulation.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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