> > > On 5/12/13 1:53 PM, Hyunjin Kim wrote: >>> >>> >>> 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 that's outdated information.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 > > The proper output is an .edr file with the decomposed energy terms you > want, so > I don't understand what "looked to produce proper output" means. Any > other > output (trajectory, coordinate, log, etc) should be identical to the > previous > run, since you're doing a rerun, not a new simulation. > > -Justin
I see. Then no I have not obtained the proper result yet. I will test what you suggested. Thanks. Hyunjin. > >> 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 >>> >> >> > > -- > ======================================== > > 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