[gmx-users] comm-grps problem gromacs 4.0.4
Oliver Grant
olymacfoogal at gmail.com
Thu Apr 29 11:42:29 CEST 2010
Hi there,
I'm running a 200ns simulation with a small trisaccharide in water. The
trisacc drifts around the box. I've tried using comm-grps = System and
comm-grps = <blank> and comm-grps = carb and what is below.
carb is the name I use in my top file and index file. For the index I
specify the groups in make_ndx and then text edit the index file and change
the name to carb. I've run this simulation on a different carb before but
with integrator set to md and it worked fine.
Any help would be very welcome
Oliver
RUN CONTROL PARAMETERS
integrator = sd
; Start time and timestep in ps
tinit = 0
dt = 0.002
nsteps = 100000000
; 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 = carb SOL Na
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 5000
nstvout = 10000
nstfout = 10000
; Checkpointing helps you continue after crashes
nstcheckpoint = 5000
; Output frequency for energies to log file and energy file
nstlog = 5000
nstenergy = 5000
; Output frequency and precision for xtc file
nstxtcout = 0
xtc-precision = 0
; 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 =
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 5
; 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 = 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 = cut-off
; cut-off lengths
rvdw-switch = 0
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; 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
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = berendsen
; Groups to couple separately
tc-grps = carb SOL Na
; Time constant (ps) and reference temperature (K)
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300
; Pressure coupling
Pcoupl = berendsen
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Random seed for Andersen thermostat
andersen_seed = 815131
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = no
gen_temp = 300
gen_seed = 1993
; OPTIONS FOR BONDS
constraints = none
; 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 = 1
; 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
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