Re: [AMBER] duplicate simulations problem

From: David A Case <>
Date: Wed, 24 Nov 2021 08:34:36 -0500

On Wed, Nov 24, 2021, Sadaf Rani wrote:

>I run a simulation of a protein-ligand complex. To verify its results I
>rerun the same simulation under the same conditions but I got
>different results. e.g. RMSF and bond distances of some key residues under
>investigation are different.
>I am unable to identify the reason for this difference although the inputs
>are the same.

Without having more information (such as your mdin file), I have to make

One common situation is to use ntt=3 and the default value of ig (which is
-1). This combination will use a different random number generator for each
run, leading (by design) to different results. It is generally recommended
that you indeed run repeated simulations in this manner, as a simple check
on reproducibility and convergence.

A second (perhaps less common) situation arises if you have irest=0 and
tempi > 0.

Third possibility: you are running parallel simulations on a CPU.

If none of these apply to you, we will need more information.


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Received on Wed Nov 24 2021 - 06:00:02 PST
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