AMBER Archive (2009)

Subject: Re: [AMBER] Velocity rescaling and ig...

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sun Jun 28 2009 - 10:35:37 CDT

it depends on how you are restarting- for example, do you irest=1 and ntx=5?
or ntx=1?
the seed is only sued in Berendsen thermostat for the initial velocity
assignment.

On Sun, Jun 28, 2009 at 10:52 AM, Cihan Aydin <cihan.aydin_at_umassmed.edu>wrote:

> Greetings AMBER community,
>
> I have a question concerning velocity rescaling and changing the ig
> value each time a simulation is restarted. So my procedure involves
> doing each nanosecond as a separate simulation and using the restart
> from one nanosecond to start the next nanosecond. I use sander.MPI so I
> set ig=-1 so that each time a new PRN series is generated. I am also
> using Berendsten thermostat in my simulations.
>
> So my question is whether changing the seed affects my simulations in
> any way? I looked through the reflector but could not come across with
> anything that answered my question (or my google search parameters were
> inefficient, if that is the case sorry for taking your time).
>
> Thank you
>
> --
> Cihan Aydin
> UMass Graduate School of Biomedical Sciences
> PhD Student @ Schiffer Lab
>
> 364 Plantation St. LRB 970M
> Worcester, MA 01605
>
> cihan.aydin_at_umassmed.edu
> +1 (508) 856-3430
>
>
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