Re: RNA simulation

From: Chris Harrison (charris5_at_gmail.com)
Date: Mon Aug 29 2011 - 19:23:07 CDT

Dear Ray,

Can you please clarify "oscillates like crazy?" That's a pretty vague
description.

And too which tutorial are you referring, and which exercise/section in
the tutorial?

Do the oscillations begin spontaneously at frame 300; and if so, is
there a something in your config that changes at frame 300? Or do the
oscillations gradually begin? The first case suggests the issue is more
likely a problem with your config/setup. The second case suggests it
may more likely be a physical problem evolving from interactions in your
structure.

Best,
Chris

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                          Voice: 217-244-1733
http://www.ks.uiuc.edu/~char              Fax:   217-244-6078
Juan Antonio Raygoza Garay <raygozag_at_email.arizona.edu> writes:
> Date: Fri, 26 Aug 2011 13:38:38 -0700
> From: Juan Antonio Raygoza Garay <raygozag_at_email.arizona.edu>
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: RNA simulation
> X-Mailer: Apple Mail (2.1084)
> 
> HI, i'm trying to run simulations in namd specifically RNA molecules and some proteins, but if i have 300 frames, always at the end the systems starts to oscillate like crazy and i've followed all the tutorial steps.
> 
> help is very much appreciated.
> 
> Ray
> 

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