VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Mar 30 2012 - 08:13:09 CDT

On Thu, Mar 29, 2012 at 4:32 PM, Phelan Jr, Frederick R. Dr.
<frederick.phelan_at_nist.gov> wrote:
> Ok, that works to a point, not quite as clean as bonds would be.
>
> But I am wondering, since you have the ix,iy,iz values internal to vmd, could not the bond rendering code not be rewritten to only display the bonds for atoms when these values for two atoms are all equal? I think that would solve it.

fred,
your understanding of what VMD does is wrong. the ix,iy,iz information
is only available inside the molfile plugin that reads lammps dump files
and then this information is used to unwrap the trajectory. VMD itself
doesn't know anything about it.

axel.

>
> Fred
>
>
>
> -----Original Message-----
> From: John Stone [mailto:johns_at_ks.uiuc.edu]
> Sent: Thursday, March 29, 2012 4:11 PM
> To: Phelan Jr, Frederick R. Dr.
> Subject: Re: vmd-l: Is there any way to stop the display of bonds for bonded atoms on opposite sides of a periodic boundary without unwrapping?
>
> Fred,
>  Create two representations with the same atom selection and they will be superimposed on top of each other.  This is actually what VMD does internally when it draws the Licorice and CPK representations.
>
> Cheers,
>  John
>
> On Thu, Mar 29, 2012 at 04:06:39PM -0400, Phelan Jr, Frederick R. Dr. wrote:
>> John,
>>
>> Both DynamicsBonds and VDW appear under "DrawingMethod" ... it seems to be a case of either/or in that regard. Is there a way to combine?
>>
>> Fred
>>
>>
>>
>> -----Original Message-----
>> From: John Stone [mailto:johns_at_ks.uiuc.edu]
>> Sent: Thursday, March 29, 2012 3:44 PM
>> To: Phelan Jr, Frederick R. Dr.
>> Cc: vmd-l_at_ks.uiuc.edu
>> Subject: Re: vmd-l: Is there any way to stop the display of bonds for bonded atoms on opposite sides of a periodic boundary without unwrapping?
>>
>> Hi,
>>   You can use the "DynamicBonds" representation to avoid this difficulty, in combination with a VDW representation.
>>
>> Cheers,
>>   John Stone
>>   vmd_at_ks.uiuc.edu
>>
>> On Thu, Mar 29, 2012 at 03:31:58PM -0400, Phelan Jr, Frederick R. Dr. wrote:
>> >    I am using the following procedure to draw LAMMPS output with bonds in
>> >    VMD:
>> >
>> >
>> >
>> >    1) Read in the LAMMPS data file: topo readlammpsdata <LAMMPS Data File
>> >    ".data"> full|molecular|bond
>> >
>> >    2) Write bond topology to psf file: animate write psf <file.psf>
>> >
>> >    3) Delete all existing molecules in memory
>> >
>> >    4) Read in the LAMMPS trajectory file < LAMMPS Trajectory File
>> >    ".lammpstrj">
>> >
>> >    5) Read in the psf file: animate read psf <file.psf>
>> >
>> >
>> >
>> >    Works great for unwrapped trajectories. However, is there any
>> >    procedure/trick to stop the display of bonds for bonded atoms on opposite
>> >    sides of a periodic boundary without unwrapping?
>> >
>> >
>> >
>> >    Thanks,
>> >
>> >    Fred
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > --------------------------------------------------------------------
>> > --
>> > ----
>> >
>> >    Frederick R. Phelan Jr., Ph.D.
>> >    Complex Fluids Group
>> >    Polymers Division
>> >    National Institute of Standards and Technology
>> >
>> >
>> > --------------------------------------------------------------------
>> > --
>> > ----
>> >
>> >    NIST, Bldg. 224/Rm. A209
>> >    100 Bureau Dr., STOP 8542
>> >    Gaithersburg, MD 20899-8542
>> >    301.975.6761 (VOX)
>> >    301.975.4924 (FAX)
>> >    frederick.phelan_at_nist.gov
>> >
>> >    My Polymers Home Page
>> >
>> >
>> >
>> >
>>
>> --
>> NIH Resource 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/       Fax: 217-244-6078
>
> --
> NIH Resource 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/       Fax: 217-244-6078 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.