VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jan 17 2014 - 11:06:26 CST

Hi,
  If you load your LAMMPS dump file in concert with a PSF, PDB, or
another file that assigns proper atom names, VMD will recognize the
hydrogens and avoid guessing extra bonds on your waters. This is
what Axel was referring to. At the moment after loading your LAMMPS
dump file, your atoms are named "1" and "2", so VMD can't do much with that...

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jan 16, 2014 at 07:01:27PM -0500, Sanjib Chowdhury wrote:
> I didn't define any bond.
> For the same model, pdb format it ok. But problem (i.e., H-H bond in water
> molecule) arises when I use lammps dump file.
> I have attached both files here.
>
> Thanks,
> Sanjib
>
> -----Original Message-----
> From: John Stone [mailto:johns_at_ks.uiuc.edu]
> Sent: Thursday, January 16, 2014 6:02 PM
> To: Sanjib Chowdhury
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Bond order cut-off value
>
> Hi,
> If the bond is defined in the structure file you loaded (e.g. PSF file),
> then VMD will draw it. To hide those bonds, you would need to delete them.
> When showing ball-stick type representations, VMD draws the bonds exactly as
> they are defined by the structure, so you'd need to delete the bonds to get
> VMD to avoid showing them. If you loaded a file format that doesn't define
> bonds, and VMD guessed the bonds, then it may be an issue with the
> assignment of atoms types, VDW radii, and the default bond guessing scheme
> VMD uses. If you provide more information about your specific case, someone
> can undoubtably suggest ways to get what you want.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Thu, Jan 16, 2014 at 05:53:54PM -0500, Sanjib Chowdhury wrote:
> > Hi,
> >
> >
> >
> > When I visualize my water model in VMD using cpk or bond drawing
> method,
> > it shows bonding between H in the water
> >
> > molecule. How I can avoid this? I guess I need to change the bond order
> > cut-off value. How can I change it in VMD?
> >
> >
> >
> > I will appreciate your suggestion.
> >
> >
> >
> > Thanks,
> >
> > Sanjib
> >
> >
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute
> for Advanced Science and Technology University of Illinois, 405 N. Mathews
> Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/