Hi justin, the out put of g_energy are like
----------------------------------------------------------------- 1 G96Angle 2 Proper-Dih. 3 Improper-Dih. 4 LJ-14 5 Coulomb-14 6 LJ-(SR) 7 LJ-(LR) 8 Disper.-corr. 9 Coulomb-(SR) 10 Coul.-recip. 11 Potential 12 Kinetic-En. 13 Total-Energy 14 Temperature 15 Pres.-DC 16 Pressure 17 Constr.-rmsd 18 Box-X 19 Box-Y 20 Box-Z 21 Volume 22 Density 23 pV 24 Enthalpy 25 Vir-XX 26 Vir-XY 27 Vir-XZ 28 Vir-YX 29 Vir-YY 30 Vir-YZ 31 Vir-ZX 32 Vir-ZY 33 Vir-ZZ 34 Pres-XX 35 Pres-XY 36 Pres-XZ 37 Pres-YX 38 Pres-YY 39 Pres-YZ 40 Pres-ZX 41 Pres-ZY 42 Pres-ZZ 43 #Surf*SurfTen 44 Box-Vel-XX 45 Box-Vel-YY 46 Box-Vel-ZZ 47 Mu-X 48 Mu-Y 49 Mu-Z 50 Coul-SR:energy-energy 51 LJ-SR:energy-energy 52 LJ-LR:energy-energy 53 Coul-14:energy-energy 54 LJ-14:energy-energy 55 Coul-SR:energy-extra34 56 LJ-SR:energy-extra34 57 LJ-LR:energy-extra34 58 Coul-14:energy-extra34 59 LJ-14:energy-extra34 60 Coul-SR:energy-rest 61 LJ-SR:energy-rest 62 LJ-LR:energy-rest 63 Coul-14:energy-rest 64 LJ-14:energy-rest 65 Coul-SR:extra34-extra34 66 LJ-SR:extra34-extra34 67 LJ-LR:extra34-extra34 68 Coul-14:extra34-extra34 69 LJ-14:extra34-extra34 70 Coul-SR:extra34-rest 71 LJ-SR:extra34-rest 72 LJ-LR:extra34-rest 73 Coul-14:extra34-rest 74 LJ-14:extra34-rest 75 Coul-SR:rest-rest 76 LJ-SR:rest-rest 77 LJ-LR:rest-rest 78 Coul-14:rest-rest 79 LJ-14:rest-rest 80 T-Protein 81 T-non-Protein 82 Lamb-Protein 83 Lamb-non-Protein When I used g_enemat with the groups.dat file like these 2 extra34 energy I got the output roup 0WARNING! could not find group (null):extra34-extra34 (0,0)in energy file WARNING! could not find group Coul-SR:extra34-energy (0,1)in energy file WARNING! could not find group LJ-SR:extra34-energy (0,1)in energy file WARNING! could not find group (null):extra34-energy (0,1)in energy file group 1WARNING! could not find group (null):energy-energy (1,1)in energy file Will select half-matrix of energies with 4 elements Last energy frame read 50000 time 10000.000 Will build energy half-matrix of 2 groups, 4 elements, over 50001 frames Segmentation fault (core dumped) Now When I changed the groups.dat like 2 energy extra34 ( change in the order of the index groups ) I got the following output, Opened ener.edr as single precision energy file Will read groupnames from inputfile Read 2 groups group 0WARNING! could not find group (null):energy-energy (0,0)in energy file WARNING! could not find group (null):energy-extra34 (0,1)in energy file group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy file Will select half-matrix of energies with 6 elements Last energy frame read 50000 time 10000.000 Will build energy half-matrix of 2 groups, 6 elements, over 50001 frames Segmentation fault (core dumped) So What is wrong ?? Is I am doing any wrong ?? 2. I am using the temp 310 so the reference temp by default is 300 Should I have to change it to 310 (-temp real 300 reference temperature for free energy calculation ) Any suggestion on these topic, is helpful to me. Thank you in advance, With best wishes and regards, Rama david. -- 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