Hi there:
I am trying to calculate the specific heat (Cp) of my protein, but I should
take into account quantum correction as indicated lately. Then, I need to
obtain from the production step the Hessian Matrix including the
eigenvectors needed to calculate the vibrational energy.
So, the point is that I set in my script the following order:
mpirun -np ${NSLOTS} mdrun_mpi -s ${NAME}-2ns.tpr -x ${NAME}-2ns.xtc -o
${NAME}-2ns.trr -c ${NAME}-2ns.gro -e ${NAME}-2ns.edr -mtx
${NAME}-hessian.mtx -nice 19 -v
and in fact, the program apparently recognizes well that a Hessian matrix
should be printed (see -mtx option below), but however I do not get such a
Hessian matrix at the end. What's happening here then? I've been looking
for any related discussion online, or whether I have to set any additional
option, maybe in the mdp file to obtain the Hesssian matrix but I've not
achieved it.
Any help, please.
Thank you very much in advance.
:-) G R O M A C S (-:
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
:-) VERSION 4.6.1 (-:
Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
Peter Kasson, Carsten Kutzner, 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) 2001-2012,2013, 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 Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
:-) mdrun_mpi (-:
Option Filename Type Description
------------------------------------------------------------
-s folded-2ns.tpr Input Run input file: tpr tpb tpa
-o folded-2ns.trr Output Full precision trajectory: trr trj cpt
-x folded-2ns.xtc Output, Opt! Compressed trajectory (portable xdr
format)
-cpi state.cpt Input, Opt. Checkpoint file
-cpo state.cpt Output, Opt. Checkpoint file
-c folded-2ns.gro Output Structure file: gro g96 pdb etc.
-e folded-2ns.edr Output Energy file
-g md.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
-tabletf tabletf.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 edsam.xvg Output, Opt. xvgr/xmgr file
-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
-ro rotation.xvg Output, Opt. xvgr/xmgr file
-ra rotangles.log Output, Opt. Log file
-rs rotslabs.log Output, Opt. Log file
-rt rottorque.log Output, Opt. Log file
-mtx folded-hessian.mtx Output, Opt! Hessian matrix <<<------------
-dn dipole.ndx Output, Opt. Index file
-multidir rundir Input, Opt., Mult. Run directory
-membed membed.dat Input, Opt. Generic data file
-mp membed.top Input, Opt. Topology file
-mn membed.ndx Input, Opt. Index file
Juan José Galano Frutos
Department of Biochemistry and
Molecular and Cellular Biology,
Faculty of Sciences,
University of Zaragoza
Pedro Cerbuna # 12, 50009
Zaragoza (Spain)
+34 976 76 28 06
Institute for Biocomputation and
Physics of Complex Systems (BIFI)
Mariano Esquillor, Edificio I + D - 50018
Zaragoza (Spain)
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