Hi Edward,
it depends a little if you want to do it on a lot of times on multiple
simulations, or only once by hand. If you just need to do it once, you
can indeed use vmd for that. Open you simulation with vmd and label a
distance between the two hydrogen atoms (you can achieve this by
pressing "2" and clicking on each of the hydrogen atom) You should see a
dashed line showing the distance between the two hydrogens at the
current snapshot.
Now go to the menu of VMD -> Graphics-> Labels
There instead of atoms, choose bonds and select your bond in the list.
You can graph this (will show the distance between your H atoms versus
time) or save it to a text file. Do the second and you'll get a file
with the first column being the number of the snapshot and the second
the distance. You can get the average now with whatever software you
want (R, shell, python...).
If you need to do this on a lot of simulations, I can recommend Biskit
(biskit.pasteur.fr). I suppose that there is also a way to do this with
ptraj, but this the Amber people might know it better than me :)
Best regards.
Peter
Edward M. wrote:
> Hello AMBER list members,
>
> I am trying to obtain the average distance between two hydrogens over
> a 1 ns simulation. I guess I need the distance at each step to be
> entered into a list and then average the list.
>
> I am using VMD but I can use any other software recommended. I assume
> this is done simply by a python script or an option in VMD; I've
> searched quite a bit and haven't found any answers.
>
> Thanks,
> Edward
>
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>
--
Peter Schmidtke
PhD Student
Dept. Physical Chemistry
Faculty of Pharmacy
University of Barcelona
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Received on Mon Sep 13 2010 - 05:00:11 PDT
