Re: Molecular Dynamics of Rigid Linear Molecules in NAMD.

From: Aron Broom (broomsday_at_gmail.com)
Date: Sun Sep 28 2014 - 10:25:13 CDT

NAMD does have the capacity to make X-H bonds completely rigid (i.e.
without a large harmonic restraint that causes timestep problems). I
wonder if that might somehow be extended to your situation?

On Sun, Sep 28, 2014 at 7:50 AM, Mike Makowski <mmakowsk_at_uci.edu> wrote:

> 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

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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