[gmx-users] Re: Hessian Matrix

#ZHAO LINA# ZHAO0139 at ntu.edu.sg
Wed Feb 3 04:10:14 CET 2010


I just simply did a change in .mdp file. Now the integrator	= nm	
after grompp, 

1) below is the error of  mdrun -s em.tpr -mtx em.mtx

Program mdrun, VERSION 4.0.7
Source code file: ../../../../src/gmxlib/smalloc.c, line: 147

Fatal error:
Not enough memory. Failed to calloc 4118944041 elements of size 4 for full_matrix
(called from file ../../../../src/mdlib/minimize.c, line 2219)

2) Seems the one run in cluster choked there like this in md.log.
Linking all bonded interactions to atoms
There are 2106 inter charge-group exclusions,
will use an extra communication step for exclusion forces for PME

The initial number of communication pulses is: X 1 Y 1
The initial domain decomposition cell size is: X 2.76 nm Y 1.07 nm

The maximum allowed distance for charge groups involved in interactions is:
                 non-bonded interactions           1.000 nm
            two-body bonded interactions  (-rdd)   1.000 nm
          multi-body bonded interactions  (-rdd)   1.000 nm

Thanks for further suggestion,


#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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