[gmx-users] weird mdrun...using gromacs 3.3.3
Naga Rajesh Tummala
rajesh.tnr at gmail.com
Tue Sep 8 19:53:09 CEST 2009
> Can you post the relevant .mdp file(s)? Are you preserving velocity
> information from the previous trajectory, or generating new velocities? Are
> any of the species in your system constrained?
>
> -Justin
>
I usually use the final output file generated by GROMACS which contain the
velocity. But, I dont preserve the velocity every timestep.
CNT, CMT are constrained. I would want to make them move only in X
direction, but I cannot make the simulation work even when they are
constrained.
title = Yo
cpp = /usr/bin/cpp
include = -I/home/rajesh/gromacs_forcefield/FMN
;include =
-I/cygdrive/c/cygwin/gromacs_forcefield/FMN_force_field
define =
; RUN CONTROL PARAMETERS
integrator = md
tinit = 0 ; start time
dt = 0.002 ; time step
nsteps = 5000 ; number of steps
init_step = 0 ; For exact run continuation or redoing
part of a run
comm-mode = None ; mode for center of mass motion
removal
nstcomm = 1 ; number of steps for center of mass
motion removal
comm-grps = ; group(s) for center of mass motion
removal
; ENERGY MINIMIZATION OPTIONS
emtol = 100 ; Force tolerance
emstep = 0.1 ; initial step-size
niter = 20000 ; Max number of iterations in
relax_shells
fcstep = 0 ; Step size (1/ps^2) for minimization
of flexible constraints
nstcgsteep = 1000 ; Frequency of steepest descents steps
when doing CG
nbfgscorr = 10
; OUTPUT CONTROL OPTIONS
nstxout = 100 ; coordinates
nstvout = 0 ; velocities
nstfout = 0 ; forces
nstcheckpoint = 10000 ; Checkpointing helps you continue
after crashes
nstlog = 100 ; Output frequency for energies to
log file
nstenergy = 1000 ; Output frequency for energies to
energy file
nstxtcout = 00 ; Output frequency for xtc file
xtc-precision = 10000 ; Output precision for xtc file
; This selects the subset of atoms for the xtc file. You can
xtc-grps = FMN SOD ; select multiple groups. By
default all atoms will be written.
energygrps = FMN CNT SOD CMT SOL ; Selection of energy
groups
; NEIGHBORSEARCHING PARAMETERS
nstlist = 10 ; nblist update frequency
ns_type = grid ; ns algorithm (simple or grid)
pbc = xyz ; Periodic boundary conditions: xyz
(default), no (vacuum);; or full (infinite systems only)
rlist = 1.4 ; nblist cut-off
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = PME ; Method for doing electrostatics
rcoulomb-switch =
rcoulomb = 1.4
epsilon-r = 1 ; Dielectric constant (DC) for cut-off
or DC of reaction field
vdw-type = switch ; Method for doing Van der Waals
rvdw-switch = 1.2 ; cut-off lengths
rvdw = 1.4
DispCorr = EnerPres ; Apply long range dispersion
corrections for Energy and Pressure
table-extension = 1 ; Extension of the potential
lookup tables beyond the cut-off
fourierspacing = 0.12 ; Spacing for the PME/PPPM FFT
grid
fourier_nx = 0 ; FFT grid size, when a value is 0
fourierspacing will be used
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
Tcoupl = nose-hoover ; Temperature coupling
tc-grps = System ; Groups to couple separately
tau_t = 0.1 ; Time constant (ps)
ref_t = 300 ; Reference temperature (K)
Pcoupl = no ; Pressure coupling
Pcoupltype = semiisotropic
tau_p = 0.5 0.0 ; Time constant (ps),
compressibility (1/bar) and reference P (bar)
compressibility = 4.5e-5 0.0
ref_p = 1.0 0.0
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = no
gen_temp = 300
gen_seed = 1993
; OPTIONS FOR BONDS
constraints = none
constraint-algorithm = lincs ; Type of constraint algorithm
unconstrained-start = no ; Do not constrain the start
configuration
Shake-SOR = no ; Use successive overrelaxation to
reduce the number of shake iterations
shake-tol = 1e-04 ; Relative tolerance of shake
lincs-order = 4 ; Highest order in the expansion of
the constraint coupling matrix
; 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-warnangle = 30 ; Lincs will write a warning to the
stderr if in one step a bond rotates over more degrees than
morse = no ; Convert harmonic bonds to morse
potentials
; ENERGY GROUP EXCLUSIONS
energygrp_excl = CNT CNT CMT CMT ; Pairs of energy
groups for which all non-bonded interactions are excluded
; Dihedral angle restraints: No, Simple or Ensemble
dihre = No
dihre-fc = 1000
dihre-tau = 0
nstdihreout = 100 ; Output frequency for dihedral
values to energy file
; Non-equilibrium MD stuff
acc-grps =
accelerate =
freezegrps = CNT CMT
freezedim = Y Y Y Y Y Y
cos-acceleration = 0
>
> Thanks
>> Rajesh
>>
>>
>>
>>
>> ------------------------------------------------------------------------
>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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