VMD-L Mailing List

From: Wang Yi (dexterwy_at_gmail.com)
Date: Tue Apr 17 2012 - 19:23:15 CDT

Ben,

The Tcl/tk functionality in VMD can help you achieve this. What you need to do is to load the DCD and PSF into the program using "mol load". And loop through the entire trajectory, update the frame in selections ($selection frame $i) and make the judgement based on your criteria. Whenever it matches, use "writepdb $selection" to write a pdf file.

Check these two links:

http://www.ks.uiuc.edu/Research/vmd/vmd-1.9/ug/node118.html

http://www.tcl.tk/man/tcl8.5/TclCmd/contents.htm

___________________________

Yi (Yves) Wang
Duke University

On 2012-4-17, at 下午7:28, Ben Rodriguez wrote:

> Hi there,
>
> I'm trying to use VMD to record the position of an atom for each frame that the atom falls within this selection expression:
> "same residue as water (within 6 of index 451) and same residue as water (within 8 of index 1518)"
>
> Ideally I would like a pdb for each frame that satisfied, but I noticed that the Save coordinates dialogue will record the position of the atom for all frames.
>
> Is there an alternate way to do what I want to do?
>
> Thanks,
>
> Ben R