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

[Juan José Galano Frutos]

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.


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                            :-)  VERSION 4.6.1  (-:

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        Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
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                Michael Shirts, Alfons Sijbers, Peter Tieleman,

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                              :-)  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)