VMD-L Mailing List

From: Sanjib Chowdhury (sanjib_at_udel.edu)
Date: Fri Jan 17 2014 - 13:01:42 CST

Yes, it is working with using the dump_modify command in lammps

dump 2 all xyz 100 dump.water-coord
dump_modify 2 element H O

Many thanks for your help.

Sanjib

-----Original Message-----
From: Axel Kohlmeyer [mailto:akohlmey_at_gmail.com]
Sent: Friday, January 17, 2014 12:59 PM
To: John Stone; Sanjib Chowdhury; Vmd l
Subject: Re: vmd-l: Bond order cut-off value

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.