Hi, I have attached the energy minimization mdp file. please look through it .
cpp = /lib/cpp ; prepocessor of the current machine define = -DFLEXIBLE ; -DPOSRES, -DPOSRES_IONS ;DFLEX_SPC; FLEXible SPC and POSition REStraints integrator = steep ; steepest descent algorithm dt = 0.005 ; time step in ps nsteps = 5000 ; number of steps emtol = 100 ; convergence criterion emstep = 0.05 ; intial step size constraints = none constraint-algorithm = lincs unconstrained-start = no ; Do not constrain the start configuration ;shake_tol = 0.0001 nstlist = 0 ; step frequency for updating neighbour list ns_type = simple ; grid ; method for nighbour searching (?) nstxout = 100 ; frequency for writing coords to output nstvout = 100 ; frequency for writing velocities to output nstfout = 0 ; frequency for writing forces to output nstlog = 100 ; frequency for writing energies to log file nstenergy = 100 ; frequency for writing energies to energy file nstxtcout = 0 ; frequency for writing coords to xtc traj xtc_grps = system ; group(s) whose coords are to be written in xtc traj energygrps = system ; group(s) whose energy is to be written in energy file pbc = no ; use pbc rlist = 1.4 ; cutoff (nm) coulombtype = cutoff ; truncation for minimisation, with large cutoff rcoulomb = 1.4 vdwtype = cut-off ; truncation for minimisation, with large cutoff rvdw = 1.4 nstcomm = 0 ; number of steps for centre of mass motion removal (in vacuo only!) Tcoupl = no Pcoupl = no "min-implicit.mdp" 40L, 2616C 1,1 Top the system I am using has the following information: PBS -l select=1:ncpus=16:mpiprocs=16 #PBS -l walltime=24:00:00 On 24 June 2018 at 13:00, Alex <nedoma...@gmail.com> wrote: > This input has no information about implicit solvent and a simple google > search immediately yields mdp examples using gbsa. As far as performance is > concerned, we don't know the specs of your machine or the size of your > system. With cutoff electrostatics and a cutoff of 5 nm, one can expect > quite a bit of scaling with system size beyond linear. > > Alex > > > > On 6/24/2018 1:04 AM, Chhaya Singh wrote: > >> 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. > -- 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.