Fwd: extracting waters from DCD

From: yi wang (yiwang_at_ks.uiuc.edu)
Date: Tue Aug 08 2006 - 16:50:55 CDT

> 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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