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