[gmx-users] double precision minimization with version 3.3
David van der Spoel
spoel at xray.bmc.uu.se
Mon Feb 27 10:09:48 CET 2006
xu yechun wrote:
> 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.
Compare the 3.2.1 and 3.3 tpr files (using gmxcheck)
Do also try to run gromacs 3.3. with the 3.2.1 tpr file
If there still is a problem then please submit a bugzilla with your tpr
files.
>
>
> 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: yechun.xu at weizmann.ac.il
>
>
> :-) 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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--
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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