[gmx-users] g_enemat problem & suggestion

[Jernej Zidar]

Hi,
  I would to calculate the interaction energies between two polymer
molecules (unit1 and unit2) and the Water_CL_NA  So the combinations are:
unit1-unit2, unit1-Water_CL_NA, unit2-Water_CL_NA. After reading the
documentation it seemed the tool g_enemat might be able to do just that in
one go.

  I created a groups.dat file with the following content:
3
unit1
unit2
Water_CL_NA

  I used "mdrun -rerun" with a modified MDP ("energygrps      = unit1 unit2
Water_CL_NA") file to generate a new EDR file as instructed by the manual.

  After doing this I run the g_enemat tool:
g_enemat -f wpoly-1-1-1-1-1-dimer-ion-npt-prod-rerun.edr -etot
wpoly-1-1-1-1-1-dimer-ion-npt-prod-ener -free -nocoullr -nocoul14 -noljlr
-nolj14 -groups groups.dat

  But it fails:
Opened wpoly-1-1-1-1-1-dimer-ion-npt-prod-rerun.edr as single precision
energy file
Will read groupnames from inputfile
Read 3 groups
group 0WARNING! could not find group (null):unit1-unit1 (0,0)in energy file
WARNING! could not find group (null):unit1-unit2 (0,1)in energy file
WARNING! could not find group (null):unit1-Water_CL_NA (0,2)in energy file
group 1WARNING! could not find group (null):unit2-unit2 (1,1)in energy file
WARNING! could not find group (null):unit2-Water_CL_NA (1,2)in energy file
group 2WARNING! could not find group (null):Water_CL_NA-Water_CL_NA (2,2)in
energy file

  It seems the tool is not performing as it should. After searching the
archives it seems the g_enemat is somewhat broken with the author stating:
"Finally finally, g_enemat was a hack. It can and should be done in a
much better
way. groups.dat should be obsolete, as it is possible to deduce the relevant
names from the energy file itself. But, as I said before, I don't have the
time now, and won't have anytime soon. Also, I don't have any particular
application now for the program ;-{" (
http://lists.gromacs.org/pipermail/gmx-users/2003-February/004123.html).

  Is g_enemat really broken? Or am I missing a detail or two not mentioned
in the manual?

thanks in advance for any explanation,
Jernej Zidar