You can find this answer in:
http://amber.ch.ic.ac.uk/archive/200308/0170.html
I do not have the pleasure of running amber 9 but
maybe is the same as amber 6 -7
From: David A. Case
<case.scripps.edu<case.scripps.edu?Subject=Re:%20AMBER:%20NTX%205%20or%207%20after%20equilibration%20in%20constant%20pressure?>>
Date: Sun Aug 17 2003 - 01:04:18 BST
On Sat, Aug 16, 2003, Majid moghaddam wrote:
*> I am trying to do MD simulation on a peptide in *
*> water(TIP3P model). I did equilibration first in *
*> constant volume, then in constant pressure. now to *
*> start production run NTX must be 5 or 7? *
For amber6, you need to set ntx=7 to force it to read the box size from
the input coordinates. This latter step is always done in amber7, so
either ntx=5 or 7 will work; (in amber7 the ntx=7 option is there only for
backwards compatiabilty with earlier scripts...ntx=5 and ntx=7 are actually
the same internally).
2007/4/9, Sandeep Kaushik <sandy.thesmitten.gmail.com>:
>
> 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..
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Received on Wed Apr 11 2007 - 06:07:20 PDT
