[gmx-users] Help for gmx enemat

[valerio di giulio]

Hi,

I have a problem with the use of "gmx enemat". I'm trying to calculate
the contribution of SH-LJ to the potential that exists between two DNA
strands with GROMACS 5.1.1. I've already got a Potential of Mean Force
doing an umbrella sampling.
For this reason I have already many files .edr each one linked to a window,
from
which I would like to extract the SH-LJ contribution but every time I use
"enemat" this is the output:

......................

GROMACS:      gmx enemat, VERSION 5.1.1
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Command line:
  gmx enemat umbrella1e.edr -ljsr

Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group Coul-SR:DNA1-DNA1 (0,0)in energy file
WARNING! could not find group LJ-SR:DNA1-DNA1 (0,0)in energy file
WARNING! could not find group Coul-SR:DNA1-DNA2 (0,1)in energy file
WARNING! could not find group LJ-SR:DNA1-DNA2 (0,1)in energy file
group 1WARNING! could not find group Coul-SR:DNA2-DNA2 (1,1)in energy file
WARNING! could not find group LJ-SR:DNA2-DNA2 (1,1)in energy file

Will select half-matrix of energies with 0 elements
Last energy frame read 500 time  500.000
Will build energy half-matrix of 2 groups, 0 elements, over 501 frames
Segmentation fault (core dumped)

...........................

Although I have written to the .mdp file:

energygrps = DNA1 DNA2

Thank you in advance,

Valerio Di Giulio