Re: rigid molecule

From: Grace Brannigan (gracebrannigan_at_gmail.com)
Date: Mon Mar 29 2010 - 14:10:40 CDT

Will fixedatoms allow you to let a molecule still translate and rotate
within the cavity? I was under the impression that fixedatoms held atoms,
well, fixed, and that to restrain just angles, bonds, and dihedrals you had
to use the col vars module...

Grace

On Sun, Mar 28, 2010 at 8:25 PM, David Tanner <guacamoleo_at_gmail.com> wrote:

> I believe what you are looking for is "fixed atoms".
>
> http://www.ks.uiuc.edu/Research/namd/2.7b2/ug/node26.html#SECTION00084300000000000000
> I believe the above link will take you to the fixed atoms parameters
> section of the online user's guide.
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> David E. Tanner
> Theoretical and Computational Biophysics Group
> 3159 Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 N. Mathews
> Urbana, IL 61801
> http://www.linkedin.com/in/davidetanner
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
> On Mar 28, 2010, at 3:34 PM, Mark M Huntress wrote:
>
> Hi, I would like to simulate the reorientation of a molecule inside a
> protein cavity, while keeping the molecule completely rigid- bonds, angles
> and dihedrals. It should only be free to translate and rotate. I tried
> rigidbonds all but that did not work, because it was still too flexible to
> move (the dihedrals). Does anyone know if there is a way to do this in NAMD?
> Thanks.
> Mark
>
>

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