[gmx-users] Segmentation fault preprocessing with pull_geometry = cylinder

[Steve Fiedler]

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