AMBER Archive (2009)

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

From: Cihan Aydin (cihan.aydin_at_umassmed.edu)
Date: Sun Jun 28 2009 - 11:08:32 CDT

Hmm its a wonder how I missed these...

My restarting parameters are irest=1 and ntx=5

So if I understand correctly, with this combination velocities are read
from the restart, not re-evaluated. So no worries, right?

Thanks,

On Sun, 2009-06-28 at 11:35 -0400, Carlos Simmerling wrote:
> 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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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> 

-- 
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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