Re: [gmx-users] implicit solvent error
sorry i attached a wrong file. this is my inputs about the implcit solvent integrator = md dt = 0.005; ps ! nsteps = 2000 ; 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 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
Re: [gmx-users] implicit solvent error
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 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 = 500 ; 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
Re: [gmx-users] implicit solvent error
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 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 = 500 ; 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
Re: [gmx-users] implicit solvent error
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 = 500 ; 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.
[gmx-users] implicit solvent error
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 = 500 ; 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.
