Hi, I am trying to simulate a protein in an implicit solvent in groamcs using amber ff99sb ildn . the mdpfile that I am using is I have shown below:
integrator = md dt = 0.001 ;0.005 ; ps ! nsteps = 5000000 ; total 5 ns. nstlog = 5000 nstxout = 0 ;1000 nstvout = 0 ;1000 nstfout = 0 ;1000 nstxtcout = 5000 nstenergy = 5000 nstlist = 10 cutoff-scheme = group rlist = 5 rvdw = 5 rcoulomb = 5 coulombtype = cut-off vdwtype = cut-off bd_fric = 0 ;ld_seed = -1 pbc = no ns_type = grid ;simple => gives domain decomposition error constraints = all-bonds lincs_order = 4 lincs_iter = 1 lincs-warnangle = 30 Tcoupl = v-rescale tau_t = 1.0 tc-grps = Protein ref_t = 310 This is the mdp file that I am using for equilibration and production run, if there is anything that I can fix in mdp file please let me know. I am getting very less speed using an implicit solvent in gromacs. is there any way to increase the speed. the speed right now I am getting is 0.47- 0.74 ns /day using one node. please help. -- 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.