Re: [AMBER] Questions on random seed

From: David A Case <>
Date: Thu, 16 Jul 2020 08:25:17 -0400

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.


>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.
> 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.


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Received on Thu Jul 16 2020 - 05:30:03 PDT
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