[gmx-users] MDRUN doesn't print Hessian Matrix as ordered
Juan José Galano Frutos
juanjogf at gmail.com
Sat Mar 18 11:46:25 CET 2017
On 3/17/17 10:35 AM, Juan José Galano Frutos wrote:
>* Thank you Justin for your replay. I've read that to compute specific
*>* heats (Cv or Cp) it is necessary calculating quantum correction (using
*>* the tool g_nmeig).
*>* Then, this tool calculates such a correction using the Hessian matrix.
*>* Is for that reason my interest in getting it.
*>* So, my question is why mdrun is not producing the indicated Hessian
*>* matrix as set up in the command line. What I am missing, maybe in the
*>* .mdp file??
*>
And I asked you about the contents of the .mdp file, which you haven't
provided.
Are you setting "integrator = nm" in it?
-Justin
Sorry Justin. As you can see below I'm using an md integrator. Then,
if I'm understanding well it is possible to obtain the required
Hessian matrix only when you perform normal modes simulations..?
If so, I have another question because although I've been reading a
lot about this quantum correction issue to exactly determine specific
heats I am not yet so clear about this:
What about the printing frequency of energy in this kind of analysis?
Is it really necessary set the higher frequency of printing energy as
possible in order to get good accuracy in this calculation or it is
not certainly so important?
Thanks again for your help.
;
; juanjo (2016)
;
title = md_prod
cpp = /lib/cpp
define =
integrator = md
dt = 0.002 ; ps !
nsteps = 1000000 ; total 2 ns.
nstcomm = 1
nstxtcout = 25000 ; each 50 ps.
xtc-precision = 25000
nstxout = 25000 ; each 50 ps.
nstvout = 25000
nstfout = 25000
nstlog = 1000
nstenergy = 1000
>* Thank
*>>>* On 3/17/17 8:20 AM, Juan José Galano Frutos wrote:
*>>* * 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.
*>* *
*>* What's in your .mdp file? IIRC the Hessian is only relevant when
doing normal
*>* modes analysis.
*>>* -Justin
*>>>* * 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 <http://www.gromacs.org>
*>* <http://www.gromacs.org <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)
*>* *>
*>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu
<https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> |
(410) 706-7441http://mackerell.umaryland.edu/~jalemkul
==================================================
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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