[gmx-users] how to change the radius of atoms in VMD

[Albert Sun]

Ran,  Thanks.
 
I followed your instructions, first load  a .gro file,  then typing comments at TkCon:
set sel [atomselect top "name C"]
sel set radius 0.5
 
Then screen showed
 
should be "set varName ?newValue?"

so I typed 
set radius 0.1  

It does not change radii of atoms, Even though I reload the .gro file, still no change on screen.
 
Is there any wrong in the above comments.
 
Thanks!
 
 
 

Ran Friedman <ran at hemi.tau.ac.il> wrote:
You should put it in the VMD console. 
Alternatively, go to extensions -> tkcon, and enter the set of commands there. You should always have pairs of commands. First, you select a set of atoms ("e.g. set sel [atomselect top "name SG or name SE"] "). Than, you set the radii. 
Also, as John Stone mentioned, you should always load a topology file (.gro or .pdb) as well as your trajectory. 
Hope that helped, 
Ran. 
Albert Sun wrote: Thanks, Ran,I am using VMD uder Windows.I could not find where should I startset sel [atomselect top "Name" ]$set sel radius Is it under Molecule or Graphics or Display? Appreciate you could advise me. Regards, Albert 
Ran Friedman <ran at hemi.tau.ac.il> wrote: Dear Albert, 
You can change the radii in VMD. Below as an example for sulphur atoms in proteins: 
set sel [atomselect top "name SG or name SE"] 
$sel set radius 1.775 
The name is the name of the atom in the topology file (in this case, it's a pdb file). 
Ran. 
Albert Sun wrote:   
Dear users, 
I am using VMD to view  .trr files from Gromacs, and found that all atoms appear in the same radius. 
I don't know if can change the radius of atoms when view the atoms, either by Gromacs or by VMD. Appreciate you can advise me. 
Many Thanks, 
Albert 

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-- ------------------------------------------------------Ran FriedmanLaser laboratory for fast reactions in biologyDepartment of biochemistryFaculty of life sciencesTel-Aviv university972-3-6409824------------------------------------------------------
 
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