From: Aaron Larsen (alarsen_at_molbio.mgh.harvard.edu)
Date: Fri Jul 31 2015 - 05:44:17 CDT
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_at_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_at_molbio.mgh.harvard.edu Mobile: 617-319-3782 FAX: 617-643-3328
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