On Sun, Jan 24, 2016 at 4:51 AM, Saman Yousuf ali <
saman.yousufali64.yahoo.com> wrote:
> Dear amber users,
> I am a beginner at amber and I have some troubles in understanding, amber
> minimization input file flags. I am using the following script for
> minimzation,
> Minimization Amber12 &cnrl imin=1, maxcyc=1000, ntmin = 2, ntx = 1, ntc
> =1, ntf = 1, ntb =1, ntp = 0, ncyc = 100, ntwx = 1000, ntwe = 0, ntpr =
> 1000, ntr = 1, cut = 10.0 &endRestarints25.0RES 1 338ENDEND
> Here in above input file, I write maxcyc 1000 with restraint of 25
> KCal/mol, is applied on protein and then minimization is followed by
> gradually relaxing restraints on both protein and counter ions (20,15,10,5)
> and then unrestraint.
> Kindly tell me, total number of minimization steps carried out by using
> these input files are 6000 0r 2000?
I must be misunderstanding your question, but as written it seems that the
answer is "neither -- at most 1000 steps of minimization is run". Also
note that the restraint is not changed as the minimization progresses.
Which means you must be running separate minimizations to do that. So if
you run 2 minimizations, and both run for the full maxcyc, you will get
2000 total minimization steps (assuming maxcyc=1000).
Note you can get all of this information just by looking at the output file.
>
> Also tell me if ncyc > maxcyc, like maxcyc is 1000 and ncyc is 5000, what
> does it mean?
>
It means that all of the minimization is steepest-descent. Look at the
ncyc description in the Amber manual and that should hopefully make things
clearer.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Jan 24 2016 - 05:00:04 PST
