[gmx-users] VMD visualization of clusters
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.
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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