Dr. David, thank you for the answer.
The command line used is:
$MPI_HOME/mpirun -np 4 $AMBERHOME/exe/sander.MPI -O -i min.in -o min.out -o
box.top -c box.crd -r min.rst -ref box.crd
The min.in is the same used in the tutorial:
&cntrl
imin=1, ntpr=100, ntwx=100, maxcyc=10000,
ntb=1,
&end
Thanks again. Moacyr.
2013/8/12 David A Case <case.biomaps.rutgers.edu>
> On Mon, Aug 12, 2013, Moacyr Comar wrote:
> >
> > I had tried run the simulations described in the tutorial A.15 (A room
> > temperature ionic liquid) with amber9 and change the ionic liquid used in
> > this tutorial by omin pf6. However, the minimization step do not produce
> > any min.out at all when I use those commands and it does when I change
> > ntb=1 for ntb=0 and igb=6. Does anyone have any idea how I can use
> boundary
> > conditions with the ionic liquid?
> >
> > the min.in of the tiutorial is:
> >
> > &cntrl
> > imin=1, ntpr=100, ntwx=100, maxcyc=10000,
> > ntb=1,
> > &end
>
> We need to see the exact command line you used. There is generally no
> reason for Amber to not create an output file (even if you inputs are
> wrong; and lack of any output file has nothing to do with the nature of
> the system you are running). Have you tried the usual: set maxcyc to 10,
> ntpr to 1 and run the job interactively?
>
> ...dac
>
>
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>
--
Prof. Dr. Moacyr Comar Junior
Universidade Federal de São João del Rei
Campus Centro-Oeste
Divinópolis - MG
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Received on Wed Aug 14 2013 - 09:00:03 PDT
