From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Tue Aug 08 2006 - 17:24:42 CDT
This sounds like a blessing! Usually, when I have to do time intensive
calculations with the atom coordinates, I save them in text format using
tcl, and then write C++ codes.
Could to tell me how/where to get this matlab code that can directly read
the binary dcd files?
On 8/8/06, yi wang <yiwang_at_ks.uiuc.edu> wrote:
> > Just to add a little more to the comment of Jerome, indeed you can't
> > write a dcd file with changing atom numbers, which is very likely the
> > case if you select only those atoms within certain distance of the
> > protein. But if you'd like to perform analysis on the coordinates,
> > Justin has a script called 'matdcd' which allows you to input the dcd
> > files into matlab and manipulate it there, which is very fast.
> > On Aug 8, 2006, at 3:55 PM, Jerome Henin wrote:
> >> Dear Nar,
> >> The DCD format imposes that all frames have the same number of atoms.
> >> So the
> >> only way I see would be to have a VMD script that does the selection,
> >> updates
> >> it for each frame and saves coordinates to separate per-frame files.
> >> Binary
> >> files (like namdbin) would use much less disk space than PDB or
> >> similar
> >> text-based formats.
> >> Jerome
> >> On Tuesday 08 August 2006 15:04, Narender Singh Maan wrote:
> >>> Dear All,
> >>> I have a trajectory file for my simulation of a protein in a big
> >>> water box.
> >>> Now to reduce the size i can extract and writeout the trajectory for
> >>> 'just
> >>> the protein' from this system by using "catdcd" but my aim is to
> >>> extract
> >>> some waters also (only those water molecules which are within 3.5
> >>> Ang. of
> >>> the protein surface...for each frame).Any suggestions would be of
> >>> great
> >>> help.
> >>> thanks
> >>> Nar
> > Thanks!
> > yi =]
> yi =]
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