[gmx-users] Segmentation Fault (core dumped) in g_mmpbsa polar energy calculation

Mark Abraham mark.j.abraham at gmail.com
Wed Jun 1 10:37:59 CEST 2016


Hi,

You can probe for memory issues by running subsets of your original
calculation, e.g. fewer trajectory frames (or however g_mmpbsa works).

Mark

On Wed, Jun 1, 2016 at 10:16 AM Pavithra <meetpavithramsc at gmail.com> wrote:

> Dear users,
>
> I have installed g_mmpbsa package for MMPBSA calculation in gromacs.
>
> When I execute MM calculations, there is no problem.
>
> But when I execute polar calculations, I get Segmentation Fault (core
> dumped) error.
>
> I tried the tutorial files, and getting the same error in polar
> calculations.
>
> The exact output is below.
>
> [pavithra at biopo3 1EBZ]$ g_mmpbsa -f 1EBZ.xtc -s 1EBZ.tpr -n 1EBZ.ndx -i
> ../polar.mdp -nomme -pbsa -decomp
>
>                            :-)  g_mmpbsa (-:
>
>                Authors: Rashmi Kumari and Andrew Lynn
>                Contribution: Rajendra Kumar
>
>        Copyright (C) 2013 - 2015  Rashmi Kumari and Andrew Lynn
>
> g_mmpbsa 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 3 of the License, or
> (at your option) any later version.
>
> g_mmpbsa is distributed in the hope that it will be useful,
> but WITHOUT ANY WARRANTY; without even the implied warranty of
> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
> GNU General Public License for more details.
>
> You should have received a copy of the GNU General Public License
> along with g_mmpbsa.  If not, see <http://www.gnu.org/licenses/>.
>
> THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
> "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
> LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
> A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
> OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
> SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
> TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
> PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
> LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
> NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
> SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
>
>                            :-)  g_mmpbsa (-:
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -f       1EBZ.xtc  Input        Trajectory: xtc trr trj gro g96 pdb cpt
>   -s       1EBZ.tpr  Input        Run input file: tpr tpb tpa
>   -i   ../polar.mdp  Input, Opt!  grompp input file with MD parameters
>   -n       1EBZ.ndx  Input, Opt!  Index file
>  -mm  energy_MM.xvg  Output, Opt. xvgr/xmgr file
> -pol      polar.xvg  Output, Opt. xvgr/xmgr file
> -apol    apolar.xvg  Output, Opt. xvgr/xmgr file
> -mmcon contrib_MM.dat  Output, Opt. Generic data file
> -pcon contrib_pol.dat  Output, Opt. Generic data file
> -apcon contrib_apol.dat  Output, Opt. Generic data file
>
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   no      Print help info and quit
> -[no]version bool   no      Print version info and quit
> -nice        int    19      Set the nicelevel
> -b           time   0       First frame (ps) to read from trajectory
> -e           time   0       Last frame (ps) to read from trajectory
> -dt          time   0       Only use frame when t MOD dt = first time (ps)
> -tu          enum   ps      Time unit: fs, ps, ns, us, ms or s
> -[no]w       bool   no      View output .xvg, .xpm, .eps and .pdb files
> -xvg         enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
> -[no]silent  bool   no      Display messages, output and errors from
> external
>                             APBS program. Only works with external APBS
>                             program
> -rad         enum   bondi   van der Waal radius type: bondi, mbondi,
> mbondi2
>                             or force-field
> -rvdw        real   0.1     Default van der Waal radius (in nm) if radius
> not
>                             found for any atom-types
> -[no]mme     bool   no      To calculate vacuum molecular mechanics energy
> -pdie        real   1       Dielectric constant of solute. Should be same
> as
>                             of polar solvation
> -[no]incl_14 bool   no      Include 1-4 atom-pairs, exclude 1-2 and 1-3
> atom
>                             pairs during MM calculation. Should be "yes"
> when
>                             groups are bonded with each other.
> -[no]focus   bool   no      To enable focusing on the specfic region of
>                             molecule, group of atoms must be provided in
>                             index file
> -[no]pbsa    bool   yes     To calculate polar and/or non-polar solvation
>                             energy
> -ndots       int    24      Number of dots per sphere in the calculation of
>                             SASA, more dots means more accuracy
> -[no]diff    bool   yes     Calculate the energy difference between two
> group
>                             otherwise only calculates for one group
> -[no]decomp  bool   yes     Decomposition of energy for each residue
>
> Reading file 1EBZ.tpr, VERSION 4.5.5-dev-20110921-e25c350 (single
> precision)
> Reading file 1EBZ.tpr, VERSION 4.5.5-dev-20110921-e25c350 (single
> precision)
>
>
>
> Enter the group number for Protein or first Protein or first group:
> Group     0 (         System) has  3218 elements
> Group     1 (        Protein) has  3129 elements
> Group     2 (      Protein-H) has  1516 elements
> Group     3 (        C-alpha) has   198 elements
> Group     4 (       Backbone) has   594 elements
> Group     5 (      MainChain) has   794 elements
> Group     6 (   MainChain+Cb) has   966 elements
> Group     7 (    MainChain+H) has   984 elements
> Group     8 (      SideChain) has  2145 elements
> Group     9 (    SideChain-H) has   722 elements
> Group    10 (    Prot-Masses) has  3129 elements
> Group    11 (    non-Protein) has    89 elements
> Group    12 (          Other) has    89 elements
> Group    13 (            BEC) has    89 elements
> Select a group: 1
> Selected 1: 'Protein'
>
>
>
> Enter the group number of Ligand or second Protein or second group:
> Group     0 (         System) has  3218 elements
> Group     1 (        Protein) has  3129 elements
> Group     2 (      Protein-H) has  1516 elements
> Group     3 (        C-alpha) has   198 elements
> Group     4 (       Backbone) has   594 elements
> Group     5 (      MainChain) has   794 elements
> Group     6 (   MainChain+Cb) has   966 elements
> Group     7 (    MainChain+H) has   984 elements
> Group     8 (      SideChain) has  2145 elements
> Group     9 (    SideChain-H) has   722 elements
> Group    10 (    Prot-Masses) has  3129 elements
> Group    11 (    non-Protein) has    89 elements
> Group    12 (          Other) has    89 elements
> Group    13 (            BEC) has    89 elements
> Select a group: 13
> Selected 13: 'BEC'
> Reading frame       0 time    0.000
> Back Off! I just backed up polar.xvg to ./#polar.xvg.1#
>
> Back Off! I just backed up contrib_pol.dat to ./#contrib_pol.dat.1#
> Segmentation fault (core dumped)
>
> I searched for the solution and found it could be memory allocation
> problem. How to be sure if its memory problem (I'm running this in centos
> desktop).
>
> Mine is 5ns simulation (xtc file)
>
> please help.
>
>
> regards,
> Pavithra.
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