From: Mike Makowski (mmakowsk_at_uci.edu)
Date: Sun Sep 28 2014 - 06:50:36 CDT
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
They explain how to keep a residue rigid.
University of California, Irvine
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Irvine, CA 92617
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On Sun, Sep 28, 2014 at 4:02 AM, Javad Noroozi <noroozi_javad_at_ymail.com>
> 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.
> Javad Noroozi,Department of Chemical Engineering,Sharif University of
> 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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