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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists