Re: [AMBER] time scales for running MD

From: David A Case <>
Date: Mon, 1 Sep 2014 08:24:05 -0400

On Mon, Sep 01, 2014, Asmita Gupta wrote:
> In 2 out of 3 trajectories, the structure is experiencing a loop residue
> backbone flipping (zeta, chi and delta), after which it remains stable.
> However, with parmbsc0, this residue flipping is not observed at all,
> neither with YIL chi correction.

One useful analysis is to see how long it took for the flip to take place in
the two trajectories where it did happen. If these are significant fractions
of the 200 ns length, then it is plausibly just a matter of chance that you
did not see such behavior in the third run. You could extend the third run
longer to see what happens.

> is 200ns enough for a good conformational sampling?

This is not sufficient in general to sample RNA loop configurations.


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Received on Mon Sep 01 2014 - 05:30:02 PDT
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