Thanks by your quick response,
Ok my problem is as follows:
** Platform: Linux, 32-bits, Gromacs 4.0.3, Ubuntu 8.10, gcc 4.3.2, kernel: 2.6.27-11-generic.
** CUDA working with several tests of the SDK on an NVIDIA 8800GT.
**Library and bin paths already “correctly” defined (at least for CUDA it works), and include the addition of gromacs/lib/openmm/
--Two different approaches:
1. - I tried to setup a simulation with FF gromos53a6, then when runing mdrun_openmm I always get a segmentation fault with no more information (output of error pasted at the end of text), it does not matter if I use mdp parameters from zephir branch or if I make my own mdp , of course simulation runs with "stock" mdrun.
2. - Using a tpr for mdrun that actually works with zephyr I tried to run mdrun_openmm and get the same segmentation fault.
Thanks.
Daniel Silva
G R O M A C S (-:
Great Red Oystrich Makes All Chemists Sane
VERSION 4.0.1 (-:
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.
/usr/local/gromacs/bin/mdrun_openmm (-:
Option Filename Type Description
------------------------------------------------------------
-s villin-rpcessed.tpr Input Run input file: tpr tpb tpa
-o asd.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 confout.gro Output Structure file: gro g96 pdb
-e ener.edr Output Energy file: edr ene
-g md.log Output Log file
-dgdl dgdl.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
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 19 Set the nicelevel
-deffnm string 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 no 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
Back Off! I just backed up md.log to ./#md.log.10#
Reading file villin-rpcessed.tpr, VERSION 4.0.3 (single precision)
Note: tpx file_version 58, software version 59
***"this note about version is not show when tpr comes from zephir preprocessing"****
Segmentation fault
****************