the improper force constants are scaled along
with all of the other terms in the force field, so
it may reflect that. look at an average structure
or average values for angles, etc and see if they
differ from normal MD.
carlos
----- Original Message -----
From: "Vlad Cojocaru" <Vlad.Cojocaru.mpi-bpc.mpg.de>
To: "amber list" <amber.scripps.edu>
Sent: Monday, February 02, 2004 4:17 PM
Subject: AMBER: nucleic acid bases nonplanar during LES sim
> Dear ambers,
> Visualizing first LES trajectories for an RNA fragment (for one copy
> out of 5) I noticed that the nucleic bases are not planar. Does that
> mean that the impropers were not applied? Is that a reason to worry
> about the simulation?
> Thank you very much
> vlad
>
> --
> Vlad Cojocaru
> Max Planck Institute for Biophysical Chemistry
> Department: 060
> Am Fassberg 11, 37077 Goettingen, Germany
> tel: ++49-551-201.1327
> e-mail: Vlad.Cojocaru.mpi-bpc.mpg.de
> home tel: ++49-551-9963204
>
>
>
>
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Received on Mon Feb 02 2004 - 22:53:00 PST
