> > > On 5/12/13 12:54 PM, Hyunjin Kim wrote: >>> >>> >>> On 5/12/13 2:25 AM, Hyunjin Kim wrote: >>>> Dear, >>>> >>>> I want to calculate LJ and Electrostatic energies between two groups >>>> defined in index.ndx during rerun with original trajectory. >>>> >>>> The following is what I tried: >>>> >>>> 1. insert "energygrps r_1 r_25" in the test.mdp file. >>>> >>>> 2. grompp -f test.mdp -c x.gro -o x.tpr -p x.top -n index.ndx >>>> >>>> 3. mdrun -nt 2 -rerun o.trr -s x.tpr -o x.trr -c x.gro -g x.log -e >>>> x.ene >>>> >>>> The simulation runs properly, but if I collect energy using g_energy, >>>> then >>>> values of all energy terms are same, although I choose different >>>> groups. >>> >>> Which specific groups did you choose? >> >> Thanks a lot. I chose residues 1 and 25. >> > > I understood that from the original post. What I was asking about was the > exact > groups you chose from the g_energy selection menu. >
When I use g_energy, I chose 4 5 6 7 8 9 10 from the below list. Thanks. 1 Bond 2 Angle 3 Ryckaert-Bell. 4 LJ-14 5 Coulomb-14 6 LJ-(SR) 7 Disper.-corr. 8 Coulomb-(SR) 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy 13 Temperature 14 Pres.-DC 15 Pressure 16 Box-X 17 Box-Y 18 Box-Z 19 Volume 20 Density 21 pV 22 Enthalpy 23 Vir-XX 24 Vir-XY 25 Vir-XZ 26 Vir-YX 27 Vir-YY 28 Vir-YZ 29 Vir-ZX 30 Vir-ZY 31 Vir-ZZ 32 Pres-XX 33 Pres-XY 34 Pres-XZ 35 Pres-YX 36 Pres-YY 37 Pres-YZ 38 Pres-ZX 39 Pres-ZY 40 Pres-ZZ 41 #Surf*SurfTen 42 Box-Vel-XX 43 Box-Vel-YY 44 Box-Vel-ZZ 45 T-System >> >>> >>>> In log file, "energygrp-flags[ 0]: 0". >>>> I think this means it calculate system energies instead of two >>>> specific >>>> groups I choose. >>>> >>> >>> Some energy terms are decomposable, most are not. There will be >>> obvious >>> differences in group names in the g_energy output. >>> >> >> I thought nonbonded energy terms were supposed to be decomposable, since >> the two groups I selected are from one in solute and one in solvent. Am >> I >> wrong? >> > > You will only get decomposed terms in the context of the interactions of > those > residues. Again, seeing the full g_energy selection menu would help us in > solving your problem. Thus far, I can see no evidence that Gromacs has > done > anything wrong, but I also haven't seen any diagnostic evidence of what > you have > tried to do. Please provide the details I have requested. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 > -- 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
