> > > On 5/12/13 1:31 PM, Hyunjin Kim wrote: >>> >>> >>> 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. >> > > Are you doing the rerun on GPU, as well, or on CPU? What happens if you > run in > serial (-nt 1)? I don't believe reruns work properly in parallel, but > maybe > that's outdated information. Does a rerun on the .xtc file produce the > desired > output? >
I am about test on rerun with -nt 1 or CPU. But, previously, I only tested rerun with -nt 2 and GPU and looked to produce proper output. However, what you mean "desired output" seems nonbonded interactions between two groups I set, which I have not. I will test rerun in CPU and even -nt 1 and see whether I got results properly. Thanks a lot for your support. Hyunjin. > -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
