Dear Priyasha,
I don’t want to seem rude, but a simple search of the manual for the term
“ioutfm” will lead you to the section in which all this flags are explained.
The question is too broad to be answered in a mailing list like that, and
can be answered with a proper look at the manual (and a search in this
mailing list for example for the explanation on why it is usually a good
idea to set ig to -1, if you don’t need an exact replicate of a simulation).
You should came back with a more defined question if you will still have
any more specific doubt about the proper value for some of these flags.
Just my 2 cents, I don’t want to seem rude, but just help you help yourself
to grow in this fascinating field :-)
On Fri, 5 May 2023 at 08:26, Priyasha Majee via AMBER <amber.ambermd.org>
wrote:
>
>
> Dear Sir/madam
>
> I am a beginner in MD. when i am reading the input scripts, i am unable
> to understand the significance of flags used and their values.
>
> Heating Equilibration - constant volume
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 1,
> ntb = 1,
> cut = 10.0,
> ntr = 0,
> ntc = 2,
> ntf = 2,
> tempi = 0.0,
> temp0 = 300.0,
> ntt = 3,
> ig = -1,
> ioutfm = 1,
> iwrap = 1,
> gamma_ln = 1.0,
> nstlim = 1000000, dt = 0.002
> ntpr = 1000, ntwx = 1000, ntwr = 1000
> /
> what does ntt , ig, ioutfm, ntx ,ntb, ntc,ntf mean?
> i have read the manual several times. but cant grasp the idea for their
> usage.
>
> simple explanation for WHY and WHEN these flags are used is appreciated.
> thanks in advance.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Domenico Marson*, Ph.D.
Ricercatore T.D. (A) | Research Fellow
Università degli Studi di Trieste | University of Trieste
Department of Engineering and Architecture (DEA)
Molecular Biology and Nanotechnology Laboratory . UniTS (MolBNL.UniTs)
Via Valerio, 10 - 34127 Trieste (Italy)
domenico.marson.dia.units.it
+39 040 5583437
Skype: domenicomars
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Received on Fri May 05 2023 - 01:30:02 PDT
