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 <mark.j.abra...@gmail.com> wrote: > On Oct 23, 2013 5:34 AM, "Nilesh Dhumal" <ndhu...@andrew.cmu.edu> 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 = 50000 >> ; 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 list gmx-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 list gmx-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 list gmx-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
