[gmx-users] Strange error in DNA simulations..
Bhanu
bhanuiitr at gmail.com
Mon Jun 15 08:23:35 CEST 2009
Hi Group,
I've tried simulating a five bp dna. It has showed many atoms missing and
some extra atoms present in the pdb file. For pdb2gmx, I used -ignh and
-mising options. Later editconf_d, genbox_d, and genion_d steps went well.
Even grompp_d worked well. But when I issued the run command for mdrun_d,
the strange result is coming, repeatedly. I have installed lam-mpi and
running gromacs in double precision. The commands I have used are..
pdb2gmx_d -f fivedna.pdb -o dna.gro -p dna.top
editconf_d -f dna.gro -bt dodecahedron -c -d 1.0 -o boxdna.gro
genbox_d -cp boxdna.gro -cs spc216.gro -p dna.top -o solvateddna.gro
neutralized the system with genion_d and grompp_d, mdrun_d with -v and
-deffnm commands. Surprisigly, everytime, it is using only two cores of my
core2quad processor, delaying the output for all experiments. For this
experiment, here is the error report which I donot understand at all!
The error report is really frightening to me!!! Here it is!
[Bhanu at localhost doublestrand]$ gedit Testfile
[Bhanu at localhost doublestrand]$ mpirun N C Testfile
NNODES=2, MYRANK=1, HOSTNAME=localhost.localdomain
NNODES=2, MYRANK=0, HOSTNAME=localhost.localdomain
NODEID=1 argc=6
NODEID=0 argc=6
:-) G R O M A C S (-:
GRowing Old MAkes el Chrono Sweat
:-) 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.
:-) mdrun_d (double precision) (-:
Option Filename Type Description
------------------------------------------------------------
-s bhanu.tpr Input Run input file: tpr tpb tpa
-o bhanu.trr Output Full precision trajectory: trr trj cpt
-x bhanu.xtc Output, Opt. Compressed trajectory (portable xdr
format)
-cpi bhanu.cpt Input, Opt. Checkpoint file
-cpo bhanu.cpt Output, Opt. Checkpoint file
-c bhanu.gro Output Structure file: gro g96 pdb
-e bhanu.edr Output Energy file: edr ene
-g bhanu.log Output Log file
-dgdl bhanu.xvg Output, Opt. xvgr/xmgr file
-field bhanu.xvg Output, Opt. xvgr/xmgr file
-table bhanu.xvg Input, Opt. xvgr/xmgr file
-tablep bhanu.xvg Input, Opt. xvgr/xmgr file
-tableb bhanu.xvg Input, Opt. xvgr/xmgr file
-rerun bhanu.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi bhanu.xvg Output, Opt. xvgr/xmgr file
-tpid bhanu.xvg Output, Opt. xvgr/xmgr file
-ei bhanu.edi Input, Opt. ED sampling input
-eo bhanu.edo Output, Opt. ED sampling output
-j bhanu.gct Input, Opt. General coupling stuff
-jo bhanu.gct Output, Opt. General coupling stuff
-ffout bhanu.xvg Output, Opt. xvgr/xmgr file
-devout bhanu.xvg Output, Opt. xvgr/xmgr file
-runav bhanu.xvg Output, Opt. xvgr/xmgr file
-px bhanu.xvg Output, Opt. xvgr/xmgr file
-pf bhanu.xvg Output, Opt. xvgr/xmgr file
-mtx bhanu.mtx Output, Opt. Hessian matrix
-dn bhanu.ndx Output, Opt. Index file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-deffnm string bhanu Set the default filename for all file options
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-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
-[no]sum bool yes Sum the energies at every step
-[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]append bool no Append to previous output files when restarting
from checkpoint
-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]glas bool no Do glass simulation with special long range
corrections
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Getting Loaded...
Reading file bhanu.tpr, VERSION 4.0.3 (double precision)
Loaded with Money
Making 1D domain decomposition 2 x 1 x 1
Steepest Descents:
Tolerance (Fmax) = 1.00000e+01
Number of steps = 10000
Step= 0, Dmax= 1.0e-02 nm, Epot= nan Fmax= 5.33517e+22, atom= 99
-------------------------------------------------------
Program mdrun_d, VERSION 4.0.3
Source code file: nsgrid.c, line: 357
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483607. It should have been within [ 0 .. 280 ]
-------------------------------------------------------
"One Ripple At a Time" (Bianca's Smut Shack)
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_d on CPU 0 out of 2
-------------------------------------------------------
Program mdrun_d, VERSION 4.0.3
Source code file: nsgrid.c, line: 357
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483607. It should have been within [ 0 .. 280 ]
-------------------------------------------------------
"One Ripple At a Time" (Bianca's Smut Shack)
Error on node 1, will try to stop all the nodes
Halting parallel program mdrun_d on CPU 1 out of 2
gcq#142: "One Ripple At a Time" (Bianca's Smut Shack)
-----------------------------------------------------------------------------
One of the processes started by mpirun has exited with a nonzero exit
code. This typically indicates that the process finished in error.
If your process did not finish in error, be sure to include a "return
0" or "exit(0)" in your C code before exiting the application.
PID 18729 failed on node n0 (127.0.0.1) with exit status 1.
-----------------------------------------------------------------------------
I tried changing the ns-type to simple, from Grid.. no success yet! Any
suggestions friends???
Bhanu Prakash.
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