From: Thomas C. Bishop (bishop_at_latech.edu)
Date: Tue Aug 11 2015 - 10:30:23 CDT
"So, I was wondering if there is a way to represent the whole trajectory as a sausage plot, like the ones usually used for NMR."
Yes, there is! This is done through vmd. You need to load a trajectory file (dcd), add labels to the bonds, angles, torsions etc. that you want to monitor and then have them exported to a graph as as function of the time stamp, The best way to do this is with a tcl script. I will email you an example script once I am at my work pc.
On Fri, Jul 31, 2015 at 6:01 AM, luca belmonte <email@example.com> wrote:
I have to represent fluctuations of small molecules around prostetic group.I began with the time step, as showed in many namd tutorials, but this is unsatisfactory for this specific case.
So, I was wondering if there is a way to represent the whole trajectory as a sausage plot, like the ones usually used for NMR.
Could you share your experience regarding this issue with me?
Thank you for all your comments,Best regards,Luca
Luca Belmonte, PhD
CIBIO - Center for Integrative BiologyUniversity of Trento
Phone: +39 0461 28 53 41Mobile: +39 328 45 81 762
Aaron Larsen, Ph.D.Harvard University Department of Chemistry and Chemical BiologyHarvard Medical School Department of GeneticsE-mail: firstname.lastname@example.orgMobile: 617-319-3782FAX: 617-643-3328
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