sorry i attached a wrong file. this is my inputs about the implcit solvent
integrator = md dt = 0.005 ; ps ! nsteps = 20000000 ; total 10 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 = simple constraints = all-bonds lincs_order = 4 lincs_iter = 1 lincs-warnangle = 30 Tcoupl = v-rescale tau_t = 1.0 tc-grps = Protein ref_t = 300 Pcoupl = no gen_vel = yes gen_temp = 300 gen_seed = 173529 ;http://www.mail-archive.com/gmx-users@gromacs.org/msg20866.html ;mine addition comm_mode = angular nstcomm = 10 ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = gbsa ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = OBC ;Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 5 ; Dielectric coefficient of the implicit solvent gb_epsilon_solvent = 80 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 gb_dielectric_offset = 0.009 sa_algorithm = Ace-approximation ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA ; The value -1 will set default value for Still/HCT/OBC GB-models. sa_surface_tension = -1 1,1 Top On 24 June 2018 at 13:17, Alex <nedoma...@gmail.com> wrote: > Your EM is unrelated to dynamics. I mean, it could, but we don't know > anything about your simulated system. I am of course assuming that your MPI > setup is optimal for gmx and you actually get to use those 16 threads, > assuming those aren't an emulation of some sort. > > > > On 6/24/2018 1:33 AM, Chhaya Singh wrote: > >> 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. > -- 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.