> > > On 5/12/13 1:14 PM, Hyunjin Kim wrote: >>> >>> >>> 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 > > Dispersion correct, PME mesh (Coul-recip), and total potential are not > decomposable. The other terms you selected should be. The fact the these > options do not appear in the .edr file indicate either (1) you did not > rerun > with the right .tpr file or (2) you analyzed the wrong .edr file. The > approach > you have suggested is correct and should result in the desired energy > groups > being present. What version of Gromacs are you using?
I use 4.6.1 with gpu. > > -Justin > >> 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 >>> >> >> > > -- > ======================================== > > 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