[gmx-users] problems generating hessian matrix
Nima S Panahi
avs at panahi.com
Tue Aug 8 03:35:10 CEST 2006
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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