[gmx-users] Hessian Matrix

Justin A. Lemkul jalemkul at vt.edu
Wed Feb 3 02:57:26 CET 2010

#ZHAO LINA# wrote:
> Hi everyone,
> I tried to use mdrun to get the .mtx file, but it does not work, I mean...no mtx file output.
> Below is the command I used in the scripts of my last two trial.
> 1)
> ## To run on 16 cpus
> #PBS -l nodes=2:ppn=8
> ## program to run
> mpirun -np $NCPUS mdrun_mpi -mtx em.mtx -deffnm em 
> 2)
> ## program to run
> mpirun -np $NCPUS mdrun_mpi -s em.tpr -mtx em.mtx 

Probably because the Hessian is only relevant when doing normal mode 
calculations (or perhaps L-BFGS minimization).  I suspect that if you're not 
using the nm integrator, then you're not going to get the Hessian.


> Thanks and best,
> lina


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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