[gmx-users] MDRUN doesn't print Hessian Matrix as ordered

[Justin Lemkul]

On 3/18/17 6:46 AM, Juan José Galano Frutos wrote:
> 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..?
>

Yes, I believe so.

> 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?
>

Sorry, no idea.  I've never done such calculations.  Hopefully someone who has 
will chime in.

-Justin

> 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 | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================