[gmx-users] Please help with all-angles constraint ption

radhika jaswal jaswalradhika at yahoo.co.in
Fri Jul 20 12:46:03 CEST 2012

Dear all,

I did NVT simulations of a number of molecules with double bond. But when i analysed the results i realised that double bond has been converted to single bond and sp2 hybridisation has also changed to sp3. I was doing with all bonds constraint option. But when i started with all angles constraint option it kept on processing on version 3.3.1 and  with many fatal errors on version 4.5.4.
I am doing with version 4.5.4 now and pasting  the parameters i am using and the errors...
the .mdp file

title = nval in energy minimisation after solvating
cpp = /usr/bin/cpp
define = -DFLEXIBLE
constraints = all-angles
constraint_algorithm = lincs
lincs_order = 6
lincs_iter = 1
integrator = steep
dt = 0.001 ; ps
nsteps = 400
nstlist = 6
ns_type = grid
rlist = 0.8
coulombtype = PME
rcoulomb = 0.8
rvdw = 0.8
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Energy Minimizing stuff
emtol = 1000.0
emstep = 0.01

and errors
/usr/local/gromacs/bin/mdrun -nice 0 -v -s nmab2_md_water_em.tpr -c nmab2_md_water_em.gro -g nmab2_md_water_em.log -o nmab2_md_water_em.trr -e nmab2_md_water_em.edr                         :-)  G  R  O  M  A  C  S  (-:

           Glycine aRginine prOline Methionine Alanine Cystine Serine

                            :-)  VERSION 4.5.4  (-:

        Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
      Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
        Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
           Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
                Michael Shirts, Alfons Sijbers, Peter Tieleman,

               Berk Hess, David van der Spoel, and Erik Lindahl.

       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
            Copyright (c) 2001-2010, The GROMACS development team at
        Uppsala University & The Royal Institute of Technology, Sweden.
            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.

                     :-)  /usr/local/gromacs/bin/mdrun  (-:

Option     Filename  Type         Description
  -s nmab2_md_water_em.tpr  Input        Run input file: tpr tpb tpa
  -o nmab2_md_water_em.trr  Output       Full precision trajectory: trr trj
  -x       traj.xtc  Output, Opt. Compressed trajectory (portable xdr format)
-cpi      state.cpt  Input, Opt.  Checkpoint file
-cpo      state.cpt  Output, Opt. Checkpoint file
  -c nmab2_md_water_em.gro  Output       Structure file: gro g96 pdb etc.
  -e nmab2_md_water_em.edr  Output       Energy file
  -g nmab2_md_water_em.log  Output       Log file
-dhdl      dhdl.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
-tableb   table.xvg  Input, Opt.  xvgr/xmgr file
-rerun    rerun.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
-tpi        tpi.xvg  Output, Opt. xvgr/xmgr file
-tpid   tpidist.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
 -px      pullx.xvg  Output, Opt. xvgr/xmgr file
 -pf      pullf.xvg  Output, Opt. xvgr/xmgr file
-mtx         nm.mtx  Output, Opt. Hessian matrix
 -dn     dipole.ndx  Output, Opt. Index file
-multidir    rundir  Input, Opt., Mult. Run directory

Option       Type   Value   Description
-[no]h       bool   no      Print help info and quit
-[no]version bool   no      Print version info and quit
-nice        int    0       Set the nicelevel
-deffnm      string         Set the default filename for all file options
-xvg         enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-[no]pd      bool   no      Use particle decompostion
-dd          vector 0 0 0   Domain decomposition grid, 0 is optimize
-nt          int    0       Number of threads to start (0 is guess)
-npme        int    -1      Number of separate nodes to be used for PME, -1
                            is guess
-ddorder     enum   interleave  DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool   yes     Check for all bonded interactions with DD
-rdd         real   0       The maximum distance for bonded interactions with
                            DD (nm), 0 is determine from initial coordinates
-rcon        real   0       Maximum distance for P-LINCS (nm), 0 is estimate
-dlb         enum   auto    Dynamic load balancing (with DD): auto, no or yes
-dds         real   0.8     Minimum allowed dlb scaling of the DD cell size
-gcom        int    -1      Global communication frequency
-[no]v       bool   yes     Be loud and noisy
-[no]compact bool   yes     Write a compact log file
-[no]seppot  bool   no      Write separate V and dVdl terms for each
                            interaction type and node to the log file(s)
-pforce      real   -1      Print all forces larger than this (kJ/mol nm)
-[no]reprod  bool   no      Try to avoid optimizations that affect binary
-cpt         real   15      Checkpoint interval (minutes)
-[no]cpnum   bool   no      Keep and number checkpoint files
-[no]append  bool   yes     Append to previous output files when continuing
                            from checkpoint instead of adding the simulation
                            part number to all file names
-maxh        real   -1      Terminate after 0.99 times this time (hours)
-multi       int    0       Do multiple simulations in parallel
-replex      int    0       Attempt replica exchange every # steps
-reseed      int    -1      Seed for replica exchange, -1 is generate a seed
-[no]ionize  bool   no      Do a simulation including the effect of an X-Ray
                            bombardment on your system

Back Off! I just backed up nmab2_md_water_em.log to ./#nmab2_md_water_em.log.15#
Getting Loaded...
Reading file nmab2_md_water_em.tpr, VERSION 4.5.4 (single precision)
Starting 8 threads
Loaded with Money

Program mdrun, VERSION 4.5.4
Source code file: domdec.c, line: 6436

Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 1.69222 nm
Change the number of nodes or mdrun option -rcon or your LINCS settings
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

"Good Music Saves your Soul" (Lemmy)

Thanks for all suggestions in advance.


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