----- Original Message ----- From: shuai shuai <[email protected]> Date: Saturday, July 10, 2010 2:27 Subject: [gmx-users] Frozen N2 in a very long tube To: [email protected]
> Hear all, > > Recently I met a strong error from gromacs. Therefore I would > like to know > whether you have experienced the same thing or what is the > reason for that. > > The system I simulated is nvt MD for N2 (with partial charge) How do you have partial charges on such a molecule? > diffusion in a > long tube (100x2.5x2.5 nm^3) at 300k. I get molecules freezed in a > small cluster after a few ns. The weird thing is that I do not have > such problem for either longer domain or short domain. The input > parameters are: I'm afraid I don't understand what you mean by "freezed in a small cluster", or a longer or shorter "domain". Mark > title = CNT > ; Preprocessor - specify a full path if necessary. > cpp = /lib/cpp > include = > define = -DPOSRES > > ; RUN CONTROL PARAMETERS > integrator = md > ; Start time and timestep in ps > tinit = 0 > dt = 0.002 > nsteps = 10000000 > ; For exact run continuation or redoing part of a run > init_step = 0 > ; mode for center of mass motion removal > comm- > mode = Linear > ; number of steps for center of mass motion removal > nstcomm = 1 > ; group(s) for center of mass motion removal > comm- > grps = > > ; LANGEVIN DYNAMICS OPTIONS > ; Friction coefficient (amu/ps) and random seed > bd- > fric = 0 > ld- > seed = 1993 > > ; ENERGY MINIMIZATION OPTIONS > ; Force tolerance and initial step-size > emtol = 100 > emstep = 0.01 > ; Max number of iterations in relax_shells > niter = 20 > ; Step size (ps^2) for minimization of flexible constraints > fcstep = 0 > ; Frequency of steepest descents steps when doing CG > nstcgsteep = 1000 > nbfgscorr = 10 > > ; OUTPUT CONTROL OPTIONS > ; Output frequency for coords (x), velocities (v) and forces (f) > nstxout = 100000 > nstvout = 100000 > nstfout = 100000 > ; Checkpointing helps you continue after crashes > nstcheckpoint = 100000 > ; Output frequency for energies to log file and energy file > nstlog = 100000 > nstenergy = 100000 > ; Output frequency and precision for xtc file > nstxtcout = 10000 > xtc- > precision = 100 > > ; nblist update frequency > nstlist = 10 > ; ns algorithm (simple or grid) > ns_type = grid > ; Periodic boundary conditions: xyz (default), no (vacuum) > ; or full (infinite systems only) > pbc = xyz > ; nblist cut-off > rlist = 1.0 > domain-decomposition = no > > ; OPTIONS FOR ELECTROSTATICS AND VDW > ; Method for doing electrostatics > coulombtype = PME > rcoulomb- > switch = 0 > rcoulomb = 1.0 > ; Relative dielectric constant for the medium and the reaction field > epsilon- > r = 1 > epsilon_rf = 1 > ; Method for doing Van der Waals > vdw- > type = Cut-off > ; cut-off lengths > rvdw- > switch = 0 > rvdw = 1.0 > ; Apply long range dispersion corrections for Energy and Pressure > DispCorr = No > ; Extension of the potential lookup tables beyond the cut-off > table- > extension = 1 > ; Seperate tables between energy group pairs > energygrp_table = > ; Spacing for the PME/PPPM FFT grid > fourierspacing = 0.12 > ; 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 = 4 > ewald_rtol = 1e-05 > ewald_geometry = 3d > epsilon_surface = 0 > optimize_fft = no > ; GENERALIZED BORN ELECTROSTATICS > ; Algorithm for calculating Born radii > gb_algorithm = 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 = 2 > ; Salt concentration in M for Generalized Born models > gb_saltconc = 0 > > ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) > implicit_solvent > = No > > ; OPTIONS FOR WEAK COUPLING ALGORITHMS > ; Temperature coupling > Tcoupl = nose-hoover > ; Groups to couple separately > tc- > grps = System > ; Time constant (ps) and reference temperature (K) > tau_t = 1 > ref_t = 303.15 > ; Pressure coupling > Pcoupl = no > Pcoupltype = isotropic > ; Time constant (ps), compressibility (1/bar) and reference P (bar) > tau_p = 5 > compressibility = 4.5e-5 > ref_p = 1 > ; Random seed for Andersen thermostat > andersen_seed = 815131 > ; OPTIONS FOR BONDS > constraints = all-bonds > ; Type of constraint algorithm > constraint-algorithm = Lincs > ; Do not constrain the start configuration > unconstrained-start = no > ; Use successive overrelaxation to reduce the number of shake > iterationsShake- > SOR = no > ; Relative tolerance of shake > shake- > tol = 1e-04 > ; Highest order in the expansion of the constraint coupling matrix > lincs- > order = 4 > ; Number of iterations in the final step of LINCS. 1 is fine for > ; normal simulations, but use 2 to conserve energy in NVE runs. > ; For energy minimization with constraints it should be 4 to 8. > lincs- > iter = 2 > ; Lincs will write a warning to the stderr if in one step a bond > ; rotates over more degrees than > lincs- > warnangle = 30 > ; Convert harmonic bonds to morse potentials > morse = no > ; Non-equilibrium MD stuff > acc- > grps = > accelerate = > freezegrps = CNT > freezedim = Y Y Y > cos-acceleration > = 0 > deform = > > > > > > > please help me if you have any suggestions or solutions. many thanks. > > > best regards > shuai > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search > before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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