Hello: energy for energygrps:I am trying to estimate the polar solvation energy of a 76 residueprotein at standard conditions. I am using the gromacs 4.5.3 dp release. I have set up a simulation with the solvated (using spce water) protein.I have defined two energygrps: Protein SOL in the *.mdp file. I have run the simulation and have then run g_energy on the *.edr file. I get the following choices from g_energy: 1 Bond 2 Angle 3 Proper-Dih. 4 Improper-Dih. 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 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 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 Mu-X 37 Mu-Y 38 Mu-Z 39 Coul-SR:Protein-Protein 40 LJ-SR:Protein-Protein 41 Coul-14:Protein-Protein 42 LJ-14:Protein-Protein 43 Coul-SR:Protein-SOL 44 LJ-SR:Protein-SOL 45 Coul-14:Protein-SOL 46 LJ-14:Protein-SOL 47 Coul-SR:SOL-SOL 48 LJ-SR:SOL-SOL 49 Coul-14:SOL-SOL 50 LJ-14:SOL-SOL 51 T-System I pick Coul-SR:Protein-SOL as a component of the polar solvation energy.I note that the energy magnitude seems extremely high: Energy Average Err.Est. RMSD Tot-Drift-------------------------------------------------------------------------------Coul-SR:Protein-SOL -8343.86 46 193.457 -192.93 (kJ/mol) This seems unreasonable to me. I wanted to understand how mdrun was calculating this value. Perhaps it is accumulating energies overmany frames. What part of the code (force.c ...) handles thiscalculation so I can verify its action and assess whether these numbersare useful. g_enemat:Also, I tried running g_enemat on this with the following groups.dat file. 2ProteinSOL I use the command: g_enemat -f ub_short.edr -e 100 and get: Opened ub_short.edr as double precision energy fileWill read groupnames from inputfileRead 2 groupsgroup 0WARNING! could not find group (null):Protein-Protein (0,0)in energy fileWARNING! could not find group (null):Protein-SOL (0,1)in energy filegroup 1WARNING! could not find group (null):SOL-SOL (1,1)in energy file Will select half-matrix of energies with 6 elementsRead frame: 1000, Time: 100.000e 100.000 Will build energy half-matrix of 2 groups, 6 elements, over 1001 framesSegmentation fault
CheersAnthony Manson Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.