Hi Cat,
You say NED, something I'm unfamiliar with, but then your input files say
neb. Are you doing Nudged Elastic Band simulations? If so, there's a
tutorial that should provide the help you need: tutorial A5.
http://ambermd.org/tutorials/advanced/tutorial5
Hope this helps,
Jason
On Fri, Aug 20, 2010 at 5:39 AM, Catein Catherine <askamber23.hotmail.com>wrote:
>
> Dear Sir/Madam,
>
>
>
> I would like to run NED in amber10. I found sander.PIMD was used in
> tutorial 5 for amber9. As no sander.PIMD can be found in my AMBERHOME/exe
> directory, I cannot run this job as in the tutorial.
>
>
>
> AMBERHOME/exe/sander.PIMD -O -i md-ala-neb-smallk_1.in -o
> md-ala-neb-smallk_1.out -p neb.prmtop -c neb.inpcrd -r
> md-ala-neb-smallk_1.rst -x md-ala-neb-smallk_1.mdcrd
>
>
>
> so, I tried to submit the job as follows by using sander.MPI. However, it
> did not works. The file stop by complaining that "Flags: MPI ***This
> version will not accept topology files that were created by addles, with
> NPARM=1 use a version compiled with -DLES"
>
>
>
> AMBERHOME/exe/sander.MPI -O -i md-ala-neb-smallk_1.in -o
> md-ala-neb-smallk_1.out -p neb.prmtop -c neb.inpcrd -r
> md-ala-neb-smallk_1.rst -x md-ala-neb-smallk_1.mdcrd
>
>
>
> >From the archive, some report the use of sander.LES.MPI, so I also give it
> a try. I submit the job in tutorial 5, section 4 as follows, but The
> output file stop at weight changes/NMR restraints.
>
>
>
> AMBERHOME/exe/sander.MPI -O -i md-ala-neb-smallk_1.in -o
> md-ala-neb-smallk_1.out -p neb.prmtop -c neb.inpcrd -r
> md-ala-neb-smallk_1.rst -x md-ala-neb-smallk_1.mdcrd
>
>
>
> Could you mind to let me know how to run the NED in amber10?
>
>
>
> Best regards,
>
>
>
> Cat
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Aug 20 2010 - 05:30:08 PDT
