Re: Molecular Dynamics of Rigid Linear Molecules in NAMD.

From: Mike Makowski (mmakowsk_at_uci.edu)
Date: Sun Sep 28 2014 - 06:50:36 CDT

Javad,

Harmonic restraints are your best bet. You'll have to include parameters in
your CHARMM FF parameter file and also in your NAMD config file. See this
CHARMM documentation:

http://www.charmmtutorial.org/index.php/Essential_CHARMM_Features#Harmonic_restraints

They explain how to keep a residue rigid.

Mike

Michael Makowski
University of California, Irvine
Department of Chemistry,
Chemical and Material Physics,
Irvine, CA 92617
Cell: 267 588 9865
Office: 949 824 5776

On Sun, Sep 28, 2014 at 4:02 AM, Javad Noroozi <noroozi_javad_at_ymail.com>
wrote:

> Mike,
>
> First, what you mean by incorrect assumptions?
>
> TraPPE and CHARMM use the same functional form for non-bonded and some
> bonded(bonds and bending) potentials. So,one can convert the parameters
> between the two force fields.The problem is that TraPPE use rigid bonds
> which is equivalent to very large spring constant in harmonic potentials. I
> want to know if there is any way to handle the rigid bonds in NAMD similar
> to virtual sites used in Gromacs tutorial?
> To my knowledge,the SHAKE algorithm implemented in NAMD works for water
> molecules only.
>
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html
>
> Bests,
> JAVAD
>
>
> _____________________
> Javad Noroozi,Department of Chemical Engineering,Sharif University of
> Technology
> Email: jnoroozi_at_che.sharif.ir
>
>
>
>
>
>
> ________________________________
> From: ‪Mike Makowski‬ ‪<mmakowsk_at_uci.edu>‬
> To: ‪Javad Noroozi‬ ‪<noroozi_javad_at_ymail.com>‬
> Cc: ‪"namd-l_at_ks.uiuc.edu"‬ ‪<namd-l_at_ks.uiuc.edu>‬
> Sent: Sunday, 28 September 2014, 11:33:10
> Subject: Re: namd-l: Molecular Dynamics of Rigid Linear Molecules in NAMD--001a11c1276c2965ae05041ec28d--

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