[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
cpt
-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
reproducibility
-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.
Radhika
More information about the gromacs.org_gmx-users
mailing list