Re: extracting waters from DCD

From: Jerome Henin (
Date: Tue Aug 08 2006 - 15:55:01 CDT

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.

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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:43:54 CST