Re: Constraint bonds that does not include hydrogrens

From: Karteek Bejagam (karteek4_at_vt.edu)
Date: Thu Dec 22 2016 - 10:00:08 CST

Thanks Jeff,

I am simulating polarizable CG martini model, where we need to constrain
two bonds from the central bead. Whose mass are 24 each.

I am looking such bonds in my simulations.

Thanks
Karteek

On 22 Dec 2016 10:38, "Jeff Comer" <jeffcomer_at_gmail.com> wrote:

> Hi Karteek,
>
> NAMD only applies rigid bonds to hydrogen atoms. It decides what is
> hydrogen based on mass. If you want to rigidify other bonds, you can
> either reduce the atom's mass to something greater than 1.0 and less
> than 3.5 or alter the code that decides whether the atom is hydrogen
> or not. See the line "} else if (atoms[atom_number-1].mass <=3.5) {"
> in Molecule.C. You can change it to something like the following for
> to get atoms named "X..." to be identified as hydrogen:
>
> } else if ( atoms[atom_number-1].mass <=3.5 ||
> atomNames[atom_number-1].atomname[0] == 'X' )
>
> I've only done this for atoms with a single bond. I'm not sure it
> works for other geometries.
>
> Regards,
> Jeff
>
> –––––––––––––––––––––––––––––––––––———————
> Jeffrey Comer, PhD
> Assistant Professor
> Institute of Computational Comparative Medicine
> Nanotechnology Innovation Center of Kansas State
> Kansas State University
> Office: P-213 Mosier Hall
> Phone: 785-532-6311
> Website: http://jeffcomer.us
>
>
> On Wed, Dec 21, 2016 at 11:00 PM, Karteek Bejagam <karteek4_at_vt.edu> wrote:
> > Dear NAMD users,
> >
> > I would like to constrain a bond that does not involve hydrogen.
> >
> > I have tried to use "rigidBonds all" but it fails.
> >
> > Can anyone help me to figure out any way to constrain the bond?
> >
> > I was looking for algorithms like SHAKE/RATTLE/SETTLE to constrain a
> bond.
> >
> > Thanks in advance,
> >
> > Karteek
>

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