Dear all,
When I submit a optimization (double precision optimization under
vacuum condition) job to GROMACS 3.3, the error information was shown as
that listed below. However, with the same structure and parameters, the
optimization can be done well using GROMACS 3.2.1. Then I submit the
optimized structure resulted from 3.2.1 to 3.3, but it still does not work
and gives out the same error information. It seems such problem can not be
caused by the program bug because I saw one information on this mailing
list that someone already optimized his structure at double precision with
3.3. So does anyone give me some clue or suggestion for my problem? Any
suggestion will be very appreciated.
Best regards
Yechun
Weizmann Institute of Science
Departement of Structural Biology
Room 610, Kimmelman Building
Rehovot 76100 Israel
Tel: 972-8-9343759 Fax: 972-8-9344159
Email: [EMAIL PROTECTED]
:-) G R O M A C S (-:
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
:-) VERSION 3.3 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2004, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun_d (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-s em1.tpr Input Generic run input: tpr tpb tpa xml
-o em1.trr Output Full precision trajectory: trr trj
-x traj.xtc Output, Opt. Compressed trajectory (portable xdr
format)
-c after_em1.gro Output Generic structure: gro g96 pdb xml
-e em1.edr Output Generic energy: edr ene
-g em1.log Output Log file
-dgdl dgdl.xvg Output, Opt. xvgr/xmgr file
-field field.xvg Output, Opt. xvgr/xmgr file
-table table.xvg Input, Opt. xvgr/xmgr file
-tablep tablep.xvg Input, Opt. xvgr/xmgr file
-rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96
pdb
-tpi tpi.xvg Output, Opt. xvgr/xmgr file
-ei sam.edi Input, Opt. ED sampling input
-eo sam.edo Output, Opt. ED sampling output
-j wham.gct Input, Opt. General coupling stuff
-jo bam.gct Output, Opt. General coupling stuff
-ffout gct.xvg Output, Opt. xvgr/xmgr file
-devout deviatie.xvg Output, Opt. xvgr/xmgr file
-runav runaver.xvg Output, Opt. xvgr/xmgr file
-pi pull.ppa Input, Opt. Pull parameters
-po pullout.ppa Output, Opt. Pull parameters
-pd pull.pdo Output, Opt. Pull data output
-pn pull.ndx Input, Opt. Index file
-mtx nm.mtx Output, Opt. Hessian matrix
-dn dipole.ndx Output, Opt. Index file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 0 Set the nicelevel
-deffnm string Set the default filename for all file options
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-np int 1 Number of nodes, must be the same as used for
grompp
-nt int 1 Number of threads to start on each node
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]sepdvdl bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-[no]multi bool no Do multiple simulations in parallel (only with
-np > 1)
-replex int 0 Attempt replica exchange every # steps
-reseed int -1 Seed for replica exchange, -1 is generate a
seed
-[no]glas bool no Do glass simulation with special long range
corrections
-[no]ionize bool no Do a simulation including the effect of an
X-Ray
bombardment on your system
Getting Loaded...
Reading file em1.tpr, VERSION 3.3 (double precision)
Loaded with Money
Polak-Ribiere Conjugate Gradients:
Tolerance (Fmax) = 1.00000e-09
Number of steps = 500000
F-max = inf on atom 1
F-Norm = inf
Step 0, Epot= nan, Fnorm= inf, Fmax= inf (atom 2)
Step 1, Epot= nan, Fnorm= nan, Fmax=0.000e+00 (atom 0)
writing lowest energy coordinates.
Polak-Ribiere Conjugate Gradients converged to Fmax < 1e-09 in 1 steps
Potential Energy = nan
Maximum force = 0.00000000000000e+00 on atom 0
Norm of force = nan
gcq#261: "It's Coming Right For Us !" (South Park)
mdp file:
; User spoel (236)
; Wed Nov 3 17:12:44 1993
; Input file
;
cpp = /lib/cpp
define = -DFLEXIBLE
constraints = none
integrator = cg (By the way, I once changed this option into
l-bfgs, but it still does not work)
nsteps = 500000
;
; Energy minimizing stuff
;
emtol = 0.000000001
emstep = 0.000001
nstcgsteep = 100
pbc = no
nstlist = 0
nstcomm = 1
ns_type = simple
rlist = 0
rcoulomb = 0
rvdw = 0
Tcoupl = no
Pcoupl = no
gen_vel = no
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