Ross,
I think I just figured it out!! I removed the &ewald section from my input
file (which was originally created to run on AMBER 8). I noticed that the
a,b,c and alpha, beta, gamma parameters have been retired and are assigned
automatically in AMBER 9. Thanks so much for all of your help!!!
Sincerely,
Justine
On Mon, Jan 12, 2009 at 4:51 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Justine,
>
> > " getting new box info from bottom of inpcrd"
> > Is the last line of one of the output files. ?
>
> If that is all the information in the output files, I.e. none of them
> produced any more than this then that could suggest that your specification
> of NTX in your input file and the value of NTB specifying periodic
> boundaries is not consistent with what is in your inpcrd / restart file.
> Are
> these periodic boundary simulations?
>
> Can you run a single simulation outside of the multisander framework? You
> may need to tweak your input slightly but you should verify that you can
> run
> a straight MD simulation with the same inputs (as close as you can) to make
> sure this is okay before switching to a multisander run where errors can
> get
> lost in obscure places.
>
> All the best
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
>
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--
-*****************************
Justine Shaw-Condo -Ph.D. Candidate
Ratner and Meade Groups
Department of Chemistry
Northwestern University
Office: 4039 Nano
Phone: 847 467 4991
Email: j-shaw.northwestern.edu
*************************************
"Great minds discuss ideas; Average minds discuss events; Small minds
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Received on Wed Jan 14 2009 - 01:15:52 PST
