AMBER Archive (2009)

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

From: Cihan Aydin (
Date: Sun Jun 28 2009 - 09:52:30 CDT

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 +1 (508) 856-3430

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