AMBER Archive (2004)

Subject: Re: AMBER: Implicit MD problem

From: David A. Case (case_at_scripps.edu)
Date: Wed Jul 14 2004 - 11:29:47 CDT

On Wed, Jul 14, 2004, yen li wrote:
>
> I am doing the simulation in baches of 1 ns each.The problem is that the
> temp v/s runlength, total energy v/s runlength and pot energy v/s run length
> plots shows kinks or drops at the points where i restart the next batch of
> the production phase. The plots for the 16 ns are attached.

Carlos is correct to ask for more information. But a guess is that when
you start a new run, you may be changing what is in the refc restraint
coordinates. If so, your restraint energy (and everything else) will have a
jump at the beginning of each nanosecond.

...dac

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