Thanks guys..
thanks for explaining all the parts...
On 4/11/07, Ross Walker <ross.rosswalker.co.uk> wrote:
>
> Hi Sandeep
>
> These are essentially there for historical reasons.
>
> NTX=7 referred to a formatted restart with box infomation. This is now
> equivalent to NTX=5. In that NTX=5 will read the box information if it
> exists in the restart file. So NTX=7 is deprecated now and NTX=5 should be
> used where NTX=7 used to be. So if you wanted you could change the benchmark
> file from NTX=7 to NTX=5 and you should get the same result.
>
> The same is true for lastist and lastrst. In earlier versions of amber it
> was sometimes necessary to specify these values when the default allocated
> memory was not enough. The benchmark required this. However with Amber 9
> these values are calculated dynamically by the code and so the user does not
> need to specify them anymore. Hence why they are no longer in the Manual.
> Although perhaps they should be in the retired namelist option section in
> the manual. I haven't checked this but if they aren't there maybe this is an
> oversight on our part. Anyway, these have been left in the benchmark input
> file to maintain backwards compatibility of the files but they are
> essentially ignored by the sander v9 executable.
>
> I hope this helps...
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | 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.
>
>
> ------------------------------
> *From:* owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] *On
> Behalf Of *Sandeep Kaushik
> *Sent:* Monday, April 09, 2007 03:36
> *To:* amber.scripps.edu
> *Subject:* AMBER: NTX=7 ?............lastist= ?...........lastrst= ?????
>
> Hi all,
> I have a few questions about the terms used in the benchmark input file in
> AMBER9..
> I want to know what does ntx = 7 stands for (i couldn't find the value "7"
> in NTX parameter ...only upto 6 have been mentioned ..
> and then second question is lastist = 4000000, & lastrst = 5000000,
> stand for what ...
> I couldn't find these values in amber 9 manual..
>
> The input file with a few modification is this:
>
> FIX (active) full dynamics ( constraint dynamics: constant volume)
> &cntrl
> ntx = 7, irest = 1,
> ntpr = 100, ntwx = 1000, ntwr = 1000,
> ntf = 2, ntc = 2, tol = 0.000001,
> cut = 8.0,
> nstlim = 1000000, dt = 0.001,
> nscm = 1000,
> ntt = 1,
> lastist = 4000000,
> lastrst = 5000000,
> /
>
> Thanks..
>
>
--
sandy_thesmitten
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Received on Sun Apr 15 2007 - 06:07:16 PDT
