[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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