Re: extracting waters from DCD

From: Jerome Henin (
Date: Wed Aug 09 2006 - 10:26:26 CDT

On Wednesday 09 August 2006 09:36, Marc Baaden wrote:
> Hi,
> the Gromacs package provides such a tool. You'd do the following:
> 1) transform your dcd trajectory to trr with catdcd
> 2) use trajorder to order the water molecules in each timeframe
> according to their distance wrt to your point of interest
> 3) use trjconv to write a subtrajectory with the system and only the
> n (maybe 200 ?) first waters
> 4) use catdcd to transform the trr back to dcd
> we have indeed used that to gain some space and preserve eg a trajectory
> of a protein and its nearest solvation shell.
> As Nicholas mentioned, you will of course loose the "identity" of the
> water molecules. So if you were to look at things like residence times
> you'd have a problem.

For residence times, you would have to build a list of relevant water
molecules for each timestep, then concatenate these lists and extract all of
these water molecules. This would remove the need for reordering residues,
but depending on the size of the system and the trajectory length, you might
not gain much as compared to analyzing the full DCD.


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