Re: [AMBER] Questions on random seed

From: Nada Afiva <>
Date: Fri, 17 Jul 2020 06:20:23 +0700

  Thank so much Prof Case,

Pada tanggal Kam, 16 Jul 2020 pukul 19.25 David A Case <> menulis:

> On Thu, Jul 16, 2020, Nada Afiva wrote:
> >I am performing multiple equilibration with random seed.
> >My question is it my command below right to perform the equlibration,
> >specifically, do I have to provide -c heat3.rst and -ref heat3.rst?
> Yes: you always need input coordinates; and always need reference
> coordinates
> if you set ntr=1.
> It is quite odd to reset the reference coordinates to be the same as the
> input
> coordinates, except (obviously) at the very first step. Be sure that this
> is
> what you want to do. Don't just follow some equilibration "recipe", but
> try
> to understand what is going on.
> Random number seeds only affect the way the Langevin thermostat works.
> Are you sure you want to set your own seed? Why? If you do, be
> double-sure
> that you don't forget to change it on every run.
> Actually I have previously performed the MD simulation on the same system
for 100 ns.
And now I will repeat the same simulation on the same system by setting
random seed.
I plan to perform 3 times simulations for the same system and my main
intention is to see whether
the second and third MD simulation converged with the first simulation.
Please correct me if it is not correct.

> >I just use the random seed option for first equlibration, not in the
> second
> >and third ones.
> >Please correct me if my understanding is wrong.
> This is wrong. Changing the default from ig=-1 should be a rare choice.
> >
Please explain what is the difference of setting ig with certain number (in
my case ig=47309)
with using ig=-1.
This is I don't understand well.

> > nstlim=50000,dt=0.001,
> Consider setting dt=0.002. Since you are running shake, you'll get much
> better equilibrarion (and production) sampling with a longer time step.
I used dt=0.001 just for equlibration step with short simulation
But for production 100 ns I used dt=0.002.

Thank you.
best regards,

> .
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Received on Thu Jul 16 2020 - 16:30:03 PDT
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