AMBER Archive (2002)

Subject: Re: message during minimization

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Wed Dec 18 2002 - 17:09:05 CST

Hello,

Thanks for the replies and sorry for not being more explicit. In the
output file this is the last thing it is written before the job stops.

Here is my input file (it is for a cubic water box L=20A, using PBC and a
cutoff of 8 A.)

Initial minimization of the water box, 20A, PBC, 8.0 cut
 &cntrl
   ntx = 1, irest = 0, ntxo = 1,
   ntpr = 1,
   ntf = 1, ntb = 1,
   cut = 8.0, scee = 1.2,
   ibelly = 0, ntr = 0,
   imin = 1,
   maxcyc = 300,
   ncyc = 50,
   ntmin = 1, dx0 = 0.1, dxm = 0.5, drms = 0.0001,
 &end

I assumed that amber will automatically use PME to calculate the
electrostatic energy (PME seems to be faster and more accurate than simple
Ewald) so I did not put anything explicit to ewald.

Here is the command to submit the job:

mpirun -np 128 $AMBERHOME/exe/sander -O -i ./box20Amin.in \
            -o ./box20Amin_128cpu.out \
            -p ./box20A.prmtop \
            -c ./box20A.prmcrd \
            -r ./box20A_128cpu.restrt \
            -ref ./box20A.prmcrd \
            -inf ./box20A.128cpu.mdinfo
\
Could this be a problem with the fact that PME is not designed to run on
128 processors? What is the limit for PME in terms of CPU's?
What is the limit for normal ewald calculations in the same terms?

Thank you,
Ioana

On Wed, 18 Dec 2002, David A. Case wrote:

> On Tue, Dec 17, 2002, Ioana Cozmuta wrote:
> >
> > APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> > using 5000.0 points per unit in tabled values
> > TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff | CHECK
> > switch(x): max rel err = 0.2088E-14 at 2.598900 | CHECK d/dx switch(x):
> > max rel err = 0.7671E-11 at 2.757160
> > ---------------------------------------------------
>
> Above is normal, and is not an error message. From the info given, I
> can't tell why the job stops.
>
> ..dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ==================================================================
>
>