Works!!
I am running production dynamics as in the tutorials (first time), so allow me to ask you if this settings are good for a medium size protein (130 aa) with 6000 waters. For 30 ns ....
production dynamics
&cntrl
imin=0, irest=1, ntx=5,
nstlim=15000000, dt=0.002,
ntc=2, ntf=2,
cut=10.0, ntb=2, ntp=1, taup=2.0,
ntpr=1000, ntwx=1000, ntwr=50000,
ntt=3, gamma_ln=2.0,
temp0=300.0,
/
Thanks!!!
Fabian
_______________________________
Fabian Glaser, PhD
Bioinformatics Knowledge Unit,
The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL
fglaser.technion.ac.il
Tel: +972 4 8293701
Fax: +972 4 8225153
On Nov 29, 2012, at 3:36 PM, Jason Swails wrote:
>
>
> On Thu, Nov 29, 2012 at 8:18 AM, Fabian Glaser <fglaser.technion.ac.il> wrote:
> Thanks Jason, much more clear now...
>
> So the following command is fine?
>
> mpirun -np 12 -hostfile $PBS_NODEFILE pmemd.MPI -O .... etc.
>
> The -np 12 is redundant if you are using $PBS_NODEFILE. In fact, if you omit the "-np 12", then you can simply change the line
>
> #PBS -l select=1:ppn=12
>
> line when you want to change the number of processors used (instead of also having to change the mpirun command as well).
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 29 2012 - 06:00:04 PST
