[gmx-users] problems generating hessian matrix
Erik Lindahl
lindahl at cbr.su.se
Tue Aug 8 09:07:35 CEST 2006
Hi,
1. Start with _really_ careful energy minimization. You need to get
the forces very close to 0 for good NMA, which usually means double
precision.
2. Use integrator=nm
2. Use the grompp "-t" flag to read the binary trajectory. If you
just use the gro file you are throwing away everything but three
decimals, which will ruin the minimization.
Cheers,
Erik
On Aug 8, 2006, at 3:35 AM, 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
> ; 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
>
>
> --
> University of Chicago
>
>
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