[gmx-users] still system exploid
Morteza Khabiri
khabiri at greentech.cz
Tue Sep 16 19:30:06 CEST 2008
Dear gmx user
I tried everything that you offer me to run my solution. I tried to assess
my system by ngmx before running. I realized that my system is exploided
befor starting EM. I tried the followinf mdp files:
1-;Enegry minimization
cpp = cpp
define = -DPSRES
integrator = steep
emtol = 1000
emstep = 0.001
nsteps = 100000
nstenergy = 10
nstxtcout = 10
nstxout = 10
nstcgsteep = 1000 ;steps
nstlist = 5
ns_type = grid
rlist = 1.0
coulombtype = cut-off
rcoulomb = 1.8
vdwtype = cut-off
rvdw = 1.0
pbc = xyz
tcoupl = berendsen
tc_grps = protein
tau_t = 0.1
ref_t = 0
pcoupl = berendsen
pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.6e-5
ref_p = 1.0
constraints = all-bonds
constraint_algorithm = shake
unconstrained_start = yes
lincs_order = 4
lincs_iter = 8
;freezegrps = Protein POPC
;freezedim = N N N N N N
gen-vel = yes
gen-temp = 0
2-
Enegry minimization
cpp = cpp
define = -DPOSRES
integrator = steep
emtol = 1000
emstep = 0.001
nsteps = 100000
nstenergy = 10
nstxtcout = 10
nstxout = 10
nstcgsteep = 1000 ;steps
nstlist = 5
ns_type = grid
rlist = 1.0
coulombtype = cut-off
rcoulomb = 1.8
vdwtype = cut-off
rvdw = 1.0
pbc = xyz
tcoupl = berendsen
tc_grps = system
tau_t = 0.1
ref_t = 0
pcoupl = berendsen
pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.6e-5
ref_p = 1.0
constraints = all-bonds
constraint_algorithm = shake
unconstrained_start = yes
lincs_order = 4
lincs_iter = 8
~
3-
title = Yo
cpp = cpp
include =
define = -DPOSRES
; RUN CONTROL PARAMETERS
integrator = l-bfgs
; Start time and timestep in ps
tinit = 0
dt = 0.001
nsteps = 10000
; For exact run continuation or redoing part of a run
init_step = 0
; mode for center of mass motion removal
comm-mode = Angular
; number of steps for center of mass motion removal
nstcomm = 1
; group(s) for center of mass motion removal
comm-grps = Protein
; LANGEVIN DYNAMICS OPTIONS
; Temperature, friction coefficient (amu/ps) and random seed
bd-temp = 300 300
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 (1/ps^2) for minimization of flexible constraints
fcstep = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep = 1000
nbfgscorr = 100
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 1000
nstvout = 1000
nstfout = 0
; Checkpointing helps you continue after crashes
nstcheckpoint = 1000
; Output frequency for energies to log file and energy file
nstlog = 500
nstenergy = 500
; Output frequency and precision for xtc file
nstxtcout = 500
59,1
Top
nstxtcout = 500
xtc-precision = 500
; 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 = 1.0
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.0
; 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 = 1.2
; 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
; 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
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 = berendsen
; Groups to couple separately
tc-grps = protein
; Time constant (ps) and reference temperature (K)
tau_t = 0.1 0.1
ref_t = 300 0.1
; Pressure coupling
Pcoupl = berendsen
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 1 1
compressibility = 4.5e-5
ref_p = 1.0 1.0
; Random seed for Andersen thermostat
andersen_seed = 815131
; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing = no
; Number of time points to use for specifying annealing in each group
annealing_npoints =
; List of times at the annealing points for each group
annealing_time =
; Temp. at each annealing point, for each group.
annealing_temp =
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
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
; rotates over more degrees than
lincs-warnangle = 30
; Convert harmonic bonds to morse potentials
morse = no
; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp_excl =
; NMR refinement stuff
; Distance restraints type: No, Simple or Ensemble
disre = No
; Force weighting of pairs in one distance restraint: Conservative or Equal
disre-weighting = Conservative
; Use sqrt of the time averaged times the instantaneous violation
disre-mixed = no
disre-fc = 1000
disre-tau = 0
; Output frequency for pair distances to energy file
nstdisreout = 100
; Orientation restraints: No or Yes
orire = no
; Orientation restraints force constant and tau for time averaging
orire-fc = 0
orire-tau = 0
orire-fitgrp =
; Output frequency for trace(SD) to energy file
nstorireout = 100
; Dihedral angle restraints: No, Simple or Ensemble
dihre = No
dihre-fc = 1000
dihre-tau = 0
; Output frequency for dihedral values to energy file
nstdihreout = 100
As you see i try all possibillity but it still did not work. I also remove
some of the molecule around the protein (which is in the center of my
soulution) by vdwd in genbox command but it did not work. Dear all, I
tried everything that you suggest me but still I am not success to run my
system.
I really don't know what should i do?
Best Regard
Morteza
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