Hi,
You observed this behavior because you DNA-complex is not centered in the box. So you have to center the molecule in the box before to do the rmsd calculation
HTH
________________________________________
De : Edjan Silva [edjan.silva.esenfar.ufal.br]
Envoyé : vendredi 1 juin 2018 16:26
À : AMBER Mailing List
Objet : [AMBER] high values ​​of RMSD during the simulation of molecular dynamics between DNA and small molecule. Does anyone explain?
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
