Re: [AMBER] simulation replication

From: Carlos Simmerling <>
Date: Mon, 26 Dec 2011 07:32:10 -0500

normally independent simulations are done to give you precision estimates
of measured values. in most cases it would not be correct to plot this as a
30ns scale. Use a 1ns scale and show all 3 simulations so readers can
compare and estimate the reliability. how much more you should do with
these depends much on the details of your project.

On Mon, Dec 26, 2011 at 5:38 AM, kanika singal <>wrote:

> Dear AmberUsers,
> I want some type of clarification regarding the simulation replication.
> Suppose, I have done 3 independent 10 ns simulation using the same starting
> structure but different ig value (random seed number). Would i call this a
> 30ns simulation and plot the results (rmsd) on a 30ns scale or should i
> call it as a 10ns simulation and plot the results on a 10 ns scale.
> Independent replication simulation essentially means to explore more
> solution space and thus can it be called a 30ns simulations.
> Thanks and Regards,
> Kanika Singal
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Received on Mon Dec 26 2011 - 05:00:02 PST
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