AMBER Archive (2009)

Subject: RE: [AMBER] minimisation with igb=10

From: Ray Luo (rayhuangluo_at_gmail.com)
Date: Mon Mar 16 2009 - 11:34:21 CDT

Carlos is correct.

PBMD is highly experimental in Amber9 and Amber10. So it doesn't make sense
to make it parallel. Wait for Amber 11 for a fully functional PBMD ... and
with parallel support too.

All the best,
Ray

==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo_at_uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf
Of Carlos Simmerling
Sent: Monday, March 16, 2009 9:05 AM
To: AMBER Mailing List
Subject: Re: [AMBER] minimisation with igb=10

I don't think so- but Ray Luo can provide a better answer to this.
as usual, though, it may take you less time to try it out than to wait for
someone to answer....

On Mon, Mar 16, 2009 at 11:56 AM, Bala subramanian <
bala.biophysics_at_gmail.com> wrote:

> Thank you,
>
> I dnt get any error. The run is complete. Is this restriction only for
> minimisation. Can i run dynamics with PB in parallel.
>
>
>
> On Mon, Mar 16, 2009 at 4:45 PM, Carlos Simmerling <
> carlos.simmerling_at_gmail.com> wrote:
>
> > I believe igb=10 does not run in parallel. do you get an actual error,
or
> > just wondering why it only uses 1 cpu?
> >
> > On Mon, Mar 16, 2009 at 11:43 AM, Bala subramanian <
> > bala.biophysics_at_gmail.com> wrote:
> >
> > > Hello,
> > >
> > > I am trying to do a minimisation with igb=10, i am submitting a
> parallel
> > > job
> > > but it runs in one processor only. The following is my input. Kindly
> > write
> > > me what is going wrong.
> > >
> > > STEP 1: minimization with PB
> > > &cntrl
> > > imin = 1, ntpr = 100, ntr = 1, restraint_wt = 50 , restraintmask =
> > > ':1-22', maxcyc =500, ncyc=300,
> > > ntmin =2, ntb = 0, igb = 10, cut = 12
> > > /
> > >
> > > command line input
> > > mpirun -np 12 sander.MPI -O -i ~/wild/min1.in -c wild_w.crd -p
> > > wild_w.top -r min1.rst -o min1.out -ref wild_w.crd
> > >
> > > Thanks,
> > > Bala
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