Re: [gmx-users] Box size increases in NPT
By "crash" I meant "explode" not "DD is impossible." Explosions don't happen because of parallelism, they happen because the steps are too large for the size of the forces. The forces required to stably expand a box from 20A to 70A seem likely to be so large that I am very skeptical that you could design such a simulation to do this with a 1fs time step. Mark On Wed, Oct 23, 2013 at 11:39 AM, Dr. Vitaly Chaban wrote: > If the job is not "very parallel", it will not crash. > > It is better to preequilibrate in NVT beforehand. Cyclopropylchloride > is probably a liquid at 290K, if the model is parametrized reasonably. > So it should not phase-separate. > > Vitaly > > > On Wed, Oct 23, 2013 at 11:29 AM, Mark Abraham > wrote: > > On Oct 23, 2013 5:34 AM, "Nilesh Dhumal" wrote: > >> > >> Hello, > >> > >> I am running a NPT simulation for cyclopropylchloride(1) in > >> 50%water(100)+50%ethanol(100) using opls force field parameter . > >> > >> After equilibration box size increases from 20 A to 70 A. > > > > Really? Seems wildly unlikely to have occurred without crashing. Over > what > > time span? How did you observe before and after? What densities do you > > measure? > > > > Mark > > > >> I used the following mdp file. > >> > >> ; RUN CONTROL PARAMETERS = > >> integrator = sd > >> ; start time and timestep in ps = > >> tinit= 0 > >> dt = 0.001 > >> nsteps = 5 > >> ; number of steps for center of mass motion removal = > >> nstcomm = 100 > >> ; OUTPUT CONTROL OPTIONS = > >> ; Output frequency for coords (x), velocities (v) and forces (f) = > >> nstxout = 0 > >> nstvout = 0 > >> nstfout = 0 > >> ; Output frequency for energies to log file and energy file = > >> nstlog = 500 > >> nstenergy= 100 > >> ; Output frequency and precision for xtc file = > >> nstxtcout= 5000 > >> xtc-precision= 1000 > >> ; NEIGHBORSEARCHING PARAMETERS = > >> ; nblist update frequency = > >> nstlist = 10 > >> ; ns algorithm (simple or grid) = > >> ns_type = grid > >> ;OPTIONS FOR TEMPERATURE COUPLING > >> tc_grps = system > >> tau_t= 0.1 > >> ref_t= 290;350 > >> ;OPTIONS FOR PRESSURE COUPLING > >> Pcoupl = berendsen > >> tau_p= 0.5 > >> compressibility = 4.5e-05 > >> ref_p= 1.0 > >> ; OPTIONS FOR BONDS = > >> constraints = hbonds > >> ; Type of constraint algorithm = > >> constraint-algorithm = Lincs > >> ; Do not constrain the start configuration = > >> unconstrained-start = no > >> ; Relative tolerance of shake = > >> shake-tol= 0.0001 > >> ; Highest order in the expansion of the constraint coupling matrix = > >> lincs-order = 12 > >> ; Lincs will write a warning to the stderr if in one step a bond = > >> ; rotates over more degrees than = > >> lincs-warnangle = 30 > >> > >> ; Periodic boundary conditions: xyz or none = > >> pbc = xyz > >> ; nblist cut-off = > >> rlist= 0.9 > >> domain-decomposition = no > >> ; OPTIONS FOR ELECTROSTATICS AND VDW = > >> ; Method for doing electrostatics = > >> coulombtype = pme > >> ;rcoulomb-switch = 0 > >> rcoulomb = 0.9 > >> ; Dielectric constant (DC) for cut-off or DC of reaction field = > >> epsilon-r= 1 > >> ; Method for doing Van der Waals = > >> vdw-type = switch > >> ; cut-off lengths= > >> rvdw-switch = 0.8 > >> rvdw = 0.9 > >> ; Apply long range dispersion corrections for Energy and Pressure = > >> DispCorr = EnerPres > >> ; Spacing for the PME/PPPM FFT grid = > >> fourierspacing = 0.1 > >> ; FFT grid size, when a value is 0 fourierspacing will be used = > >> fourier_nx = 0 > >> fourier_ny = 0 > >> fourier_nz = 0 > >> ; EWALD/PME/PPPM parameters = > >> pme_order= 6 > >> ewald_rtol = 1e-06 > >> epsilon_surface = 0 > >> optimize_fft = no > >> ; Free energy control stuff > >> free_energy = no > >> > >> > >> Nilesh > >> > >> > >> > >> -- > >> gmx-users mailing listgmx-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 listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please sear
Re: [gmx-users] Box size increases in NPT
If the job is not "very parallel", it will not crash. It is better to preequilibrate in NVT beforehand. Cyclopropylchloride is probably a liquid at 290K, if the model is parametrized reasonably. So it should not phase-separate. Vitaly On Wed, Oct 23, 2013 at 11:29 AM, Mark Abraham wrote: > On Oct 23, 2013 5:34 AM, "Nilesh Dhumal" wrote: >> >> Hello, >> >> I am running a NPT simulation for cyclopropylchloride(1) in >> 50%water(100)+50%ethanol(100) using opls force field parameter . >> >> After equilibration box size increases from 20 A to 70 A. > > Really? Seems wildly unlikely to have occurred without crashing. Over what > time span? How did you observe before and after? What densities do you > measure? > > Mark > >> I used the following mdp file. >> >> ; RUN CONTROL PARAMETERS = >> integrator = sd >> ; start time and timestep in ps = >> tinit= 0 >> dt = 0.001 >> nsteps = 5 >> ; number of steps for center of mass motion removal = >> nstcomm = 100 >> ; OUTPUT CONTROL OPTIONS = >> ; Output frequency for coords (x), velocities (v) and forces (f) = >> nstxout = 0 >> nstvout = 0 >> nstfout = 0 >> ; Output frequency for energies to log file and energy file = >> nstlog = 500 >> nstenergy= 100 >> ; Output frequency and precision for xtc file = >> nstxtcout= 5000 >> xtc-precision= 1000 >> ; NEIGHBORSEARCHING PARAMETERS = >> ; nblist update frequency = >> nstlist = 10 >> ; ns algorithm (simple or grid) = >> ns_type = grid >> ;OPTIONS FOR TEMPERATURE COUPLING >> tc_grps = system >> tau_t= 0.1 >> ref_t= 290;350 >> ;OPTIONS FOR PRESSURE COUPLING >> Pcoupl = berendsen >> tau_p= 0.5 >> compressibility = 4.5e-05 >> ref_p= 1.0 >> ; OPTIONS FOR BONDS = >> constraints = hbonds >> ; Type of constraint algorithm = >> constraint-algorithm = Lincs >> ; Do not constrain the start configuration = >> unconstrained-start = no >> ; Relative tolerance of shake = >> shake-tol= 0.0001 >> ; Highest order in the expansion of the constraint coupling matrix = >> lincs-order = 12 >> ; Lincs will write a warning to the stderr if in one step a bond = >> ; rotates over more degrees than = >> lincs-warnangle = 30 >> >> ; Periodic boundary conditions: xyz or none = >> pbc = xyz >> ; nblist cut-off = >> rlist= 0.9 >> domain-decomposition = no >> ; OPTIONS FOR ELECTROSTATICS AND VDW = >> ; Method for doing electrostatics = >> coulombtype = pme >> ;rcoulomb-switch = 0 >> rcoulomb = 0.9 >> ; Dielectric constant (DC) for cut-off or DC of reaction field = >> epsilon-r= 1 >> ; Method for doing Van der Waals = >> vdw-type = switch >> ; cut-off lengths= >> rvdw-switch = 0.8 >> rvdw = 0.9 >> ; Apply long range dispersion corrections for Energy and Pressure = >> DispCorr = EnerPres >> ; Spacing for the PME/PPPM FFT grid = >> fourierspacing = 0.1 >> ; FFT grid size, when a value is 0 fourierspacing will be used = >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> ; EWALD/PME/PPPM parameters = >> pme_order= 6 >> ewald_rtol = 1e-06 >> epsilon_surface = 0 >> optimize_fft = no >> ; Free energy control stuff >> free_energy = no >> >> >> Nilesh >> >> >> >> -- >> gmx-users mailing listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] Box size increases in NPT
On Oct 23, 2013 5:34 AM, "Nilesh Dhumal" wrote: > > Hello, > > I am running a NPT simulation for cyclopropylchloride(1) in > 50%water(100)+50%ethanol(100) using opls force field parameter . > > After equilibration box size increases from 20 A to 70 A. Really? Seems wildly unlikely to have occurred without crashing. Over what time span? How did you observe before and after? What densities do you measure? Mark > I used the following mdp file. > > ; RUN CONTROL PARAMETERS = > integrator = sd > ; start time and timestep in ps = > tinit= 0 > dt = 0.001 > nsteps = 5 > ; number of steps for center of mass motion removal = > nstcomm = 100 > ; OUTPUT CONTROL OPTIONS = > ; Output frequency for coords (x), velocities (v) and forces (f) = > nstxout = 0 > nstvout = 0 > nstfout = 0 > ; Output frequency for energies to log file and energy file = > nstlog = 500 > nstenergy= 100 > ; Output frequency and precision for xtc file = > nstxtcout= 5000 > xtc-precision= 1000 > ; NEIGHBORSEARCHING PARAMETERS = > ; nblist update frequency = > nstlist = 10 > ; ns algorithm (simple or grid) = > ns_type = grid > ;OPTIONS FOR TEMPERATURE COUPLING > tc_grps = system > tau_t= 0.1 > ref_t= 290;350 > ;OPTIONS FOR PRESSURE COUPLING > Pcoupl = berendsen > tau_p= 0.5 > compressibility = 4.5e-05 > ref_p= 1.0 > ; OPTIONS FOR BONDS = > constraints = hbonds > ; Type of constraint algorithm = > constraint-algorithm = Lincs > ; Do not constrain the start configuration = > unconstrained-start = no > ; Relative tolerance of shake = > shake-tol= 0.0001 > ; Highest order in the expansion of the constraint coupling matrix = > lincs-order = 12 > ; Lincs will write a warning to the stderr if in one step a bond = > ; rotates over more degrees than = > lincs-warnangle = 30 > > ; Periodic boundary conditions: xyz or none = > pbc = xyz > ; nblist cut-off = > rlist= 0.9 > domain-decomposition = no > ; OPTIONS FOR ELECTROSTATICS AND VDW = > ; Method for doing electrostatics = > coulombtype = pme > ;rcoulomb-switch = 0 > rcoulomb = 0.9 > ; Dielectric constant (DC) for cut-off or DC of reaction field = > epsilon-r= 1 > ; Method for doing Van der Waals = > vdw-type = switch > ; cut-off lengths= > rvdw-switch = 0.8 > rvdw = 0.9 > ; Apply long range dispersion corrections for Energy and Pressure = > DispCorr = EnerPres > ; Spacing for the PME/PPPM FFT grid = > fourierspacing = 0.1 > ; FFT grid size, when a value is 0 fourierspacing will be used = > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > ; EWALD/PME/PPPM parameters = > pme_order= 6 > ewald_rtol = 1e-06 > epsilon_surface = 0 > optimize_fft = no > ; Free energy control stuff > free_energy = no > > > Nilesh > > > > -- > gmx-users mailing listgmx-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 listgmx-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
