[gmx-users] Re: Re:double precision minimization with version 3.3
Florian Haberl
Florian.Haberl at chemie.uni-erlangen.de
Tue Mar 21 18:44:25 CET 2006
Hi,
On Tuesday 21 March 2006 18:11, Yechun Xu wrote:
> Dear gmx users,
>
> First, I'd like to thank David's suggestion. It is not a bug of the
> program but a problem of installation. Now it is fixed and works fine.
>
> I met another problem about the double precision minimization (used for
> NMA later) with l-bfgs in version 3.3. It seems the optimization will never
> finish. The protein only includes 604 atoms (in vacuum) and the
> optimization started almost three weeks ago but only reach something like:
> "Step 29403607, Epot=-3.927499e+03, Fnorm=2.169e-01, Fmax=1.699e+00 (atom
> 451)"
>
> So my question is that the l-bfgs optimization does take very long time or
> there is some problem with my mdps file? Any suggestions are very
> appreciated!
>
> cpp = /lib/cpp
> define = -DFLEXIBLE
> constraints = none
> integrator = l-bfgs
> nsteps = 50000000
> ;
> ; Energy minimizing stuff
> ;
> emtol = 0.000000001
> emstep = 0.000000001
Your step size is too small
standard are here (see handbook chapter 7.3):
emtol = 100.0 [KJ/(mol nm)]
emstep = 0.01 [nm]
so try this and if it doesn`t work, change the standard parameters with factor
10 or 100.
>
> nstlist = 10
> ;nstcomm = 1
> ns_type = simple
> rlist = 1.6
> rcoulomb_switch = 1.2
> rcoulomb = 1.4
> rvdw_switch = 1.2
> rvdw = 1.4
> vdwtype = Shift
> coulombtype = Shift
> pbc = no
>
> OR mdp file like this:
> cpp = /lib/cpp
> define = -DFLEXIBLE
> constraints = none
> integrator = l-bfgs
> nsteps = 50000000
> ;
> ; Energy minimizing stuff
> ;
> emtol = 0.000001
> emstep = 0.000001
>
> nstlist = 10
> nstcomm = 1
> ns_type = grid
> rlist = 1.6
> rcoulomb = 1.4
> rvdw = 1.4
> vdwtype = Shift
> coulombtype = PME
> Tcoupl = no
> Pcoupl = no
> gen_vel = no
>
>
>
>
> 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
>
> >>> 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
> >> 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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> >> _______________________________________________
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> >> http://www.gromacs.org/mailman/listinfo/gmx-users
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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
> >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Greetings,
Florian
--
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Florian Haberl
Computer-Chemie-Centrum
Universitaet Erlangen/ Nuernberg
Naegelsbachstr 25
D-91052 Erlangen
Mailto: florian.haberl AT chemie.uni-erlangen.de
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