VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jan 17 2014 - 11:59:07 CST

On Fri, Jan 17, 2014 at 12:06 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> 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...

with the latest LAMMPS plugin for VMD, the element information can be
communicated via the LAMMPS dump using the dump_modify element option
and then using a custom dump file that dumps the element name in
addition. VMD will then pick up that information and the bond
determination heuristics will do a better guess at effective atom
radii and avoid H-H bonds.

axel.

>
> 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/ 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.