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
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
