[gmx-users] still system exploid
Justin A. Lemkul
jalemkul at vt.edu
Tue Sep 16 21:18:27 CEST 2008
What kind of solvent are you using, anyway? Your original post said it was an
organic solvent, but in one of your .mdp files you've got POPC, which would
imply a membrane. What kind of system are we dealing with?
The bottom line is that you have severe atomic overlap, and you might be able to
get some clue from the LINCS warnings (which I believe you quoted before) as to
where things start to fall apart.
If solvent atoms near the protein are the problem, you could temporarily
increase the VDW radius of, say, carbon during the genbox stage, and increase
your box size slightly (since the solvent will contract during a simulation). A
bit of trial and error may be in order there.
-Justin
Morteza Khabiri wrote:
> 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
>
>
>
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
More information about the gromacs.org_gmx-users
mailing list