"Not working" is too vague a symptom for anyone to guess what the problem is, sorry.
Mark On Oct 24, 2013 9:39 AM, "Santu Biswas" <santu.biswa...@gmail.com> wrote: > dear users, > > I am performing 500ps mdrun in vacuum for polypeptide(formed > by 10-residues leucine) using gromacs_4.5.5(double-precision) using > opls-aa/L force field.Input file for 500ps mdrun is given below > > > title = peptide in vaccum > cpp = /lib/cpp > > ; RUN CONTROL > integrator = md > comm_mode = ANGULAR > nsteps = 500000 > dt = 0.001 > ; NEIGHBOR SEARCHING > nstlist = 0 > ns_type = simple > pbc = no > rlist = 0 > ; OUTPUT CONTROL > nstxout = 1000 > nstvout = 1000 > nstxtcout = 0 > nstlog = 1000 > constraints = none > nstenergy = 1000 > ; OPTION FOR ELECTROSTATIC AND VDW > rcoulomb = 0 > ; Method for doing Van der Waals > rvdw = 0 > ; OPTIONS FOR WEAK COUPLING ALGORITHMS > tcoupl = V-rescale > tc_grps = Protein > tau_t = 0.1 > ref_t = 300 > gen_vel = yes > gen_temp = 300 > > Using the 500ps trajectory if i run g_hbond_d for calculating the number of > hydrogen bonds as a function of time using index file(where atom O and atom > N H is used) it is not working. > Also if i used g_rdf_d with pbc=no using the 500ps trajectory it is also > not working. > I do not know why this is happening. > > ------ > santu > -- > 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
