[gmx-users] Frozen N2 in a very long tube
shuai shuai
banshuai at gmail.com
Fri Jul 9 18:27:31 CEST 2010
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) 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:
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 iterations
Shake-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
More information about the gromacs.org_gmx-users
mailing list