[gmx-users] problems generating hessian matrix
David van der Spoel
spoel at xray.bmc.uu.se
Tue Aug 8 07:52:27 CEST 2006
Nima S Panahi wrote:
> PLEASE HELP ASAP I need this to work. Thanks in advance
> I run
>
> /usr/local/gromacs/bin/grompp_d -f argon.mdp -c argon.gro -p topol.top
> -o file.tpr
>
> followed by
>
> /usr/local/gromacs/bin/mdrun_d -s file.tpr -o file.trr -c mdout.gro -e
> ener.edr -g md.log -mtx nm.mtx
>
> but there is not nm.mtx created
>
>
> my arong.mdp looks like:
> ; VARIOUS PREPROCESSING OPTIONS
> title =
> cpp = /lib/cpp
> include =
> define =
>
> ; RUN CONTROL PARAMETERS
> integrator = md
integrator = nm
> ; Start time and timestep in ps
> tinit = 0
> dt = 0.002
> nsteps = 25000
> ; 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 =
>
> ; LANGEVIN DYNAMICS OPTIONS
> ; Temperature, friction coefficient (amu/ps) and random seed
> bd-temp = 120
> 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 = 10
>
> ; OUTPUT CONTROL OPTIONS
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout = 10000
> nstvout = 10000
> nstfout = 0
> ; Checkpointing helps you continue after crashes
> nstcheckpoint = 1000
> ; Output frequency for energies to log file and energy file
> nstlog = 100
> nstenergy = 100
> ; Output frequency and precision for xtc file
> nstxtcout = 100
> xtc-precision = 1000
> ; 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 = 1
> ; 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 = 2.5
> domain-decomposition = no
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype = Cut-off
> rcoulomb-switch = 0
> rcoulomb = 2.5
> ; 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 = 2.5
> ; 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
> ; 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 = No
> ; Groups to couple separately
> tc-grps = system
> ; Time constant (ps) and reference temperature (K)
> tau-t = 0.1
> ref-t = 120
> ; Pressure coupling
> Pcoupl = No
> Pcoupltype = Isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau-p = 1
> compressibility = 5e-5
> ref-p = 1
> ; Random seed for Andersen thermostat
> andersen_seed = 815131
>
> ; SIMULATED ANNEALING
> ; Type of annealing for each temperature group (no/single/periodic)
> annealing =
> ; 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 = no
> gen-temp = 120
> gen-seed = 173529
>
>
> my argon.go looks like:
> Argon
> 13
> 1AR AR 1 -0.033 0.081 0.257 0.1866 -0.2544 0.5213
> 2AR AR 2 -0.034 -0.140 -0.353 0.3855 -0.4920 0.8269
> 3AR AR 3 0.355 -0.067 -0.367 -0.0668 0.4193 0.6096
> 4AR AR 4 0.311 -0.125 0.176 0.2093 -0.6313 0.9828
> 5AR AR 5 -0.042 0.366 0.008 -0.3232 -0.4550 -0.9181
> 6AR AR 6 -0.308 -0.321 -0.171 0.7523 0.3857 0.3527
> 7AR AR 7 0.501 0.124 -0.072 0.8134 -0.6625 0.8499
> 8AR AR 8 0.570 -0.241 -0.088 0.3273 0.9660 -0.6965
> 9AR AR 9 0.282 0.265 0.192 -0.8447 0.3001 0.6661
> 10AR AR 10 -0.050 -0.244 0.089 -0.0174 0.2349 0.8296
> 11AR AR 11 0.134 0.051 -0.088 -0.0855 0.6894 -0.7369
> 12AR AR 12 0.215 -0.331 -0.145 -0.3998 -0.9677 0.2980
> 13AR AR 13 -0.236 0.042 -0.072 0.2268 -0.5540 0.4119
> 6.65637 6.65637 6.65637
>
> my topol.top looks like:
>
> [ defaults ]
> ; nbfunc comb-rule
> 1 3
>
> [ atomtypes ]
> ; full atom descriptions are available in ffoplsaa.atp
> ; name bond_type mass charge ptype sigma epsilon
> AR AR 39.94800 0 A 0.34 .9974
>
> [ molecule_type ]
> Argon 1
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> 1 AR 1 AR AR 1 0
>
>
> [ system ]
> ; Name
> Argon
>
> [ molecules ]
> ; Compound #mols
> Argon 13
>
>
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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