[gmx-users] comm-grps problem gromacs 4.0.4

[Oliver Grant]

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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