[gmx-users] Frozen N2 in a very long tube
Mark Abraham
mark.abraham at anu.edu.au
Sat Jul 10 09:32:11 CEST 2010
----- Original Message -----
From: shuai shuai <banshuai at gmail.com>
Date: Saturday, July 10, 2010 2:27
Subject: [gmx-users] Frozen N2 in a very long tube
To: gmx-users at gromacs.org
> 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
> --
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