Re: AMBER: Simulated annealing ...vlimit problem

From: Carlos Simmerling <>
Date: Mon, 17 May 2004 13:08:56 -0400

have you minimized the structure first? can you do "normal
MD" on this one too, not the protonated and hydrated one?
try to only change 1 thing at a time or else it is hard to track
down the problem.

your heating phase will be very fast and that can cause lots
of problems, especially with a poor initial structure.
why not add a step to heat to 600K over some period
of time?


> I have also done the normal MD on the same structure which went fine, but
> in this case I have protonated it and also hydrated it.

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Received on Mon May 17 2004 - 18:53:00 PDT
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