[gmx-users] timestep for CG simulation

[Ashish Gupta]

Hi all,
   
     I am trying to use the coarse grained simulation of Marrink
(http://md.chem.rug.nl/~marrink/coarsegrain.html). I am looking at
a simple system a box containing water, DPC and hexadecane.  I shall be
glad if somebody help me choose the proper timestep for these simulation.

  The suggested value of the timestep is 0.05 ps. With this value of 
timestep the simulation
seem to be running fine for some steps (some thousands of steps) and 
then I get segmentation
fault error. Why is this so ?  Also if I reduce the timestep to 0.005 ps 
then the simulations run
fine.
Thanks in advance for any help,
Ashish.


Below is my *.mdp file


; VARIOUS PREPROCESSING OPTIONS =
title                    = Yo
cpp                      = /lib/cpp
include                  =
define                   =

; RUN CONTROL PARAMETERS =
integrator               = md
; start time and timestep in ps =
tinit                    = 0.0
dt                       = 0.05
nsteps                   = 100000
; number of steps for center of mass motion removal =
nstcomm                  = 1


; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout                  = 2000
nstvout                  = 2000
nstfout                  = 0
; Output frequency for energies to log file and energy file =
nstlog                   = 1000
nstenergy                = 1000
; Output frequency and precision for xtc file =
nstxtcout                = 1000
xtc_precision            = 1000
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps                 =
; Selection of energy groups =
energygrps               = DPC W

; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist                  = 10
; ns algorithm (simple or grid) =
ns_type                  = grid
; Periodic boundary conditions: xyz or none =
pbc                      = xyz
; nblist cut-off         =
rlist                    = 1.2
domain-decomposition     = no

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype              = Shift
rcoulomb_switch          = 0.0
rcoulomb                 = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r                = 20
; Method for doing Van der Waals =
vdw_type                 = Shift
; cut-off lengths        =
rvdw_switch              = 0.9
rvdw                     = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr                 = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing           = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx               = 10
fourier_ny               = 10
fourier_nz               = 10
; EWALD/PME/PPPM parameters =
pme_order                = 4
ewald_rtol               = 1e-05
epsilon_surface          = 0
optimize_fft             = no

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
tcoupl                   = Berendsen
; Groups to couple separately =
tc-grps                  = DPC HD W
; Time constant (ps) and reference temperature (K) =
tau_t                    = 1.0 1.0 1.0
ref_t                    = 300 300 300
; Pressure coupling      =
Pcoupl                   = Berendsen
Pcoupltype               = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p                    = 1.0
compressibility          = 1e-5
ref_p                    = 1.0


; SIMULATED ANNEALING CONTROL =
annealing                = no no no
; Time at which temperature should be zero (ps) =
;zero_temp_time           = 0

; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel                  = no
gen_temp                 = 300
gen_seed                 = 473529