namd-l: Re: sausage plot for a namd trajectory in vmd

Hi Luca,

"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.

Best,

Aaron

On Fri, Jul 31, 2015 at 6:01 AM, luca belmonte <lucabelmonte@gmail.com> wrote:

Dear all,

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 Biology

University of Trento

Phone: +39 0461 28 53 41

Mobile: +39 328 45 81 762

Aaron Larsen, Ph.D.

Harvard University Department of Chemistry and Chemical Biology

Harvard Medical School Department of Genetics

E-mail: alarsen@molbio.mgh.harvard.edu

Mobile: 617-319-3782

FAX: 617-643-3328