Bug #51

the failure of double precision minimization

Added by Xu Yechun over 13 years ago. Updated over 13 years ago.

Target version:
Affected version - extra info:
Affected version:


When I submit a optimization (double precision optimization with vacuum force
field) job to GROMACS 3.3, the error information was shown as that listed
elow. However, with the same structure and parameters, the optimization can be
done well using GROMACS 3.2.1. Then I submit the structure optimized by 3.2.1
to 3.3 or the tpr file produced by 3.2.1 to 3.3, but it still does not work
and gives out the same error information.

(sorry. I do want to submit the tpr files together with this bug report but I
don't find a right place to do it. If you do need the tpr file, pls email me
to get them)

:-)  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 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
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 seed
-[no]glas bool no Do glass simulation with special long range
-[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

em1_321.tpr (565 KB) em1_321.tpr tpr file produced with gromacs3.2.1 Xu Yechun, 02/28/2006 10:26 AM


#1 Updated by David van der Spoel over 13 years ago

Please submit the 3.2.1 tpr file that works in 3.2.1 but not in 3.3, using bugzilla.

#2 Updated by Xu Yechun over 13 years ago

Created an attachment (id=20)
tpr file produced with gromacs3.2.1

#3 Updated by David van der Spoel over 13 years ago

Works for me in double precision on Mac OS X and on Linux/Opteron (and gives the
same result):

Back Off! I just backed up ener.edr to ./#ener.edr.1#
Polak-Ribiere Conjugate Gradients:
Tolerance (Fmax) = 1.00000e-09
Number of steps = 500000
F-max = 1.61936e+10 on atom 153
F-Norm = 2.29001e+10

Back Off! I just backed up traj.trr to ./#traj.trr.1#
Step 0, Epot=8.038375e+07, Fnorm=3.075e+08, Fmax=1.619e+10 (atom 153)
Step 1, Epot=8.034673e+07, Fnorm=3.072e+08, Fmax=1.618e+10 (atom 153)
Step 2, Epot=8.028692e+07, Fnorm=3.070e+08, Fmax=1.617e+10 (atom 153)
Step 3, Epot=8.019037e+07, Fnorm=3.066e+08, Fmax=1.615e+10 (atom 153)

and so on.

How did you compile the code?

#4 Updated by David van der Spoel over 13 years ago

Any comment on the compilation? Or more information?

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