RE: AMBER: NTX=7 ?............lastist= ?...........lastrst= ?????

From: Ross Walker <>
Date: Tue, 10 Apr 2007 15:53:19 -0700

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

|\oss Walker

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From: [] On Behalf Of
Sandeep Kaushik
Sent: Monday, April 09, 2007 03:36
Subject: AMBER: NTX=7 ?............lastist= ?...........lastrst= ?????

Hi all,
I have a few questions about the terms used in the benchmark input file in
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)
   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,


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Received on Wed Apr 11 2007 - 06:07:44 PDT
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