[gmx-users] VMD visualization of clusters

Justin Lemkul jalemkul at vt.edu
Tue Nov 20 00:47:31 CET 2018

On 11/19/18 8:57 AM, Rahma Dahmani wrote:
> Hi GMX users,
> After visualization of one of my clusters generated by g-cluster command in
> gromacs , i couldn't change the representation type in VMD from lines to
> new cartoon or secondary structure....
> so i am wondering if this is related to the structure of cluster ? ... why
> i can visualize the cluster only in lines ?

VMD guesses its renderings based on interatomic distances. If you have 
multiple structures overlaid on one another, it's going to fail to 
distinguish one structure from another. Ask for tips on the VMD mailing 
list if you're having trouble with VMD.



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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