Re: removing water from DCD

From: Shirley Hui (
Date: Wed Jul 20 2005 - 20:25:51 CDT

If you have use of Matlab, you can use matDCD.

Call readDCD, ead into Matlab only the atoms you want (i.e. specify atoms
numbers of the non-water atoms from the pdb file you used to run the

Then call writedcd to write to another DCD file with only the non-water
atoms you read into Matlab above.


----- Original Message -----
From: "Stern, Julie" <>
To: <>
Sent: Wednesday, July 20, 2005 8:49 PM
Subject: namd-l: removing water from DCD

    What is the best way to remove water
from the DCD file after it has been created?
Are there any postprocessing tools for this?



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