[gmx-users] double precision minimization with version 3.3

xu yechun ycxu222 at hotmail.com
Mon Feb 27 10:04:05 CET 2006

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

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 
  -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 
-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
         -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 
   -[no]glas   bool     no  Do glass simulation with special long range
 -[no]ionize   bool     no  Do a simulation including the effect of an 
                            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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