Hi, Thanks for the reply. I have included it and rerun my system. Still problem prevails.
On Fri, 20 Dec, 2019, 7:22 AM Bratin Kumar Das, <177cy500.bra...@nitk.edu.in> wrote: > Hi > You have to mention energygrous in your .mdp file and rerun the > simulation. The details you'll get in gromacs protein- ligand complex > tutorial. > > On Thu 19 Dec, 2019, 11:11 PM Suvardhan Jonnalagadda, < > j.su.vard...@gmail.com> wrote: > > > Hi All, > > > > *"GROMACS: VERSION 4.5.5; Precision: single"* > > I have performed an md simulation for 1 time step, on a single molecule > > with 17 atoms. I want to calculate all the energies (angle, dihedrals, > > bonds, 1-4 interactions), and compare. However, I am not able to get the > > LJ-14 interactions energy from the '*.edr'* file. When i searched in the > > manual, I came across *'gmx enemat'* command. > > I gave the following command > > > > *'gmx enemat -f nvt_single.edr -groups groups.dat -lj14'* > > In the groups.dat I have entered the molecule name (as in the *.itp > > *file). > > > > So, the error and warnings I get after the above command are as follows: > > > > > > > > > > > > > > > > > > > > *" group 16WARNING! could not find group Coul-SR:C16-C16 (16,16)in > energy > > fileWARNING! could not find group LJ-SR:C16-C16 (16,16)in energy > > fileWARNING! could not find group LJ-14:C16-C16 (16,16)in energy fileWill > > select half-matrix of energies with 0 elementsLast energy frame read 0 > > time 0.000 Will build energy half-matrix of 17 groups, 0 > > elements, over 1 framesSegmentation fault (core dumped) "* > > Is this a bug? or am I missing something? > > Also, what does 'LJ(SR)' term in the energies include? In my case, I have > > only one molecule. So, what does this LJ short range include? > > > > Thank you, > > > > Best regards, > > Vardhan > > -- > > 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. > > > -- > 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. > -- 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.