Hi, 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,
lina
#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.
-Justin
> Thanks and best,
>
> lina
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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