Re: [AMBER] RMSD plot query

From: Hai Nguyen <>
Date: Thu, 14 Jul 2016 10:57:10 -0400

On Thu, Jul 14, 2016 at 10:29 AM, esther nehu <>

> Hello Amber Users
> I have an RMSD plot for a polyamide duplex. In most papers i came across
> they have shown that the rmsd plot is almost in the same alignment but the
> plot i got is different from what i expected. So does this mean that my
> system is not stable during the whole simulation?

You can visualize your structure in VMD, Pymol, ... to know if you
structure is stable.
It's hard to tell from your plot (what's timescale? which atom mask you
used for RMSD, do you use the same mask with other papers?,
what's unit for x, y axis? ...)


> What conclusion can i
> draw from the plot?
This really depend on what you're trying to learn from your simulation.

> Thanks
> Esther
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Received on Thu Jul 14 2016 - 08:00:03 PDT
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