Re: [AMBER] checkpoint on Amber within batch job

From: David A Case <>
Date: Thu, 23 Jan 2014 15:22:16 -0500

On Thu, Jan 23, 2014, James Maier wrote:
> This depends on whether you are using a thermostat or barostat. Some
> thermostats and especially barostats can give you artifacts if you restart
> too quickly with the same random seed (ig flag). Setting ig differently
> for each restart helps alleviate that. But if you're running say, 20 ns at
> a time, it might not be a big deal.

Be *very* careful: even with long time spans between restarts, running
Langevin thermostats (ntt=3) without changes the random number seed for
each restart will lead to bad results. Using ig=-1 avoids all of these
problems, and for the most most users' needs.


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Received on Thu Jan 23 2014 - 12:30:05 PST
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