From: Carlos Simmerling <>
Date: Thu, 14 Jan 2021 06:22:06 -0500

the conclusion you draw from a simulation should be reproducible. if your 3
runs behave differently, then the results may not be reliable. you should
look into the details, perhaps analyzing more than just RMSD. can you
visually compare the 3 runs to see what structure differences lead to the
calculated RMSD differences? it may be something not important, such as
fraying of the DNA ends, or it may be very important. This is the
challenging part of simulation research.

On Thu, Jan 14, 2021 at 6:15 AM Syeda Amna Arshi <>

> Hello,
> I did the same simulation for three times with identical conditions but the
> resultant rmsd plots are quite different from each other. Is this normal??
> if yes is there any way to plot the average rmsd of these three simulations
> or we should take only one of them (but on what basis should we select the
> same)?
> --
> Sincerely,
> *Syeda Amna Arshi*
> *Ph.D. Scholar*
> Multidisciplinary Centre For Advanced Research and Studies
> Jamia Millia Islamia
> Delhi-110025
> 7737638065
> [image: Image result for save world by plant][image: Image result for save
> world by plant white background]
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Received on Thu Jan 14 2021 - 03:30:02 PST
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