Dear all,
On transitioning from Gromacs version 3.3.3 to 4.0.3, I have encountered
a segmentation fault (output below) preprocessing a constraint force
calculation, while using the pull code with the "pull_geometry =
cylinder" option in the mdp file. This problem appears is reproducible
on 32 and 64 bit architecture systems, and is present using both single
and double precision versions of the grompp executable. Alternative
pull options (constraint, umbrella, and constant_force) also generated
this error. This calculation can be successfully run using Gromacs
version 3.3.3 with the below ppa file options.
Suggestions would be appreciated.
Thank you,
Steve Fiedler
Gromacs 4.0.3 mdp pull options:
pull = constraint
pull_geometry = cylinder
pull_r1 = 1
pull_r0 = 1.5
pull_dim = N N Y
pull_vec1 = 0 0 1
pull_group1 = Buk
pull_group0 = Ref
pull_init1 = .4
Gromacs 3.3.3 ppa file:
runtype = constraint
reftype = dynamic
r = 1.
rc = 1.5
pull_dim = N N Y
constraint_direction = 0 0 1
group_1 = BUK
reference_group = Ref
constraint_distance1 = 0.400
Preprocessing output for Gromacs 4.0.3 calculation:
bash-3.2$ grompp_d -n index.ndx
:-) G R O M A C S (-:
Grunge ROck MAChoS
:-) VERSION 4.0.3 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, 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.
:-) grompp_d (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-f grompp.mdp Input, Opt. grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c conf.gro Input Structure file: gro g96 pdb tpr tpb tpa
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
-n index.ndx Input, Opt! Index file
-p topol.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o topol.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file: edr ene
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-[no]v bool yes Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with
virtual
sites
-maxwarn int 0 Number of allowed warnings during input
processing
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Ignoring obsolete mdp entry 'title'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#
checking input for internal consistency...
processing topology...
Generated 224 of the 378 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.125
Generated 377 of the 378 1-4 parameter combinations
Excluding 1 bonded neighbours molecule type 'ADMP'
Excluding 1 bonded neighbours molecule type 'ACHO'
Excluding 1 bonded neighbours molecule type 'AWAT'
Excluding 3 bonded neighbours molecule type 'BUKY'
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Making dummy/rest group for T-Coupling containing 6848 elements
Pull group 0 'Ref' has 2266 atoms
Pull group 1 'Buk' has 60 atoms
Making dummy/rest group for Acceleration containing 6848 elements
Making dummy/rest group for Freeze containing 6848 elements
Making dummy/rest group for Energy Mon. containing 6848 elements
Making dummy/rest group for VCM containing 6848 elements
Number of degrees of freedom in T-Coupling group rest is 13752.00
Making dummy/rest group for User1 containing 6848 elements
Making dummy/rest group for User2 containing 6848 elements
Making dummy/rest group for XTC containing 6848 elements
Making dummy/rest group for Or. Res. Fit containing 6848 elements
Making dummy/rest group for QMMM containing 6848 elements
T-Coupling has 1 element(s): rest
Energy Mon. has 1 element(s): rest
Acceleration has 1 element(s): rest
Freeze has 1 element(s): rest
User1 has 1 element(s): rest
User2 has 1 element(s): rest
VCM has 1 element(s): rest
XTC has 1 element(s): rest
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 27x36x63, spacing 0.119 0.117 0.120
Segmentation fault
--
Steve Fiedler, Ph.D.
Research Fellow
Department of Mechanical Engineering
The University of Michigan
2024 G.G. Brown
2350 Hayward St.
Ann Arbor, MI 48109-2125
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