Re: [AMBER] high values ​​of RMSD during the simulation of molecular dynamics between DNA and small molecule. Does anyone explain?

From: Carlos Simmerling <>
Date: Fri, 1 Jun 2018 10:33:14 -0400

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On Fri, Jun 1, 2018, 10:26 AM Edjan Silva <>

> I performed a simulation between a small molecule and B-DNA. The result of
> the RMSD is this of the figure. By analyzing the structure at these points,
> it appears that some atoms get far away from the DNA, inside the box. Why
> does this happen? Does this make my simulation invalid?
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Received on Fri Jun 01 2018 - 08:00:03 PDT
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