Re: Removing some water from a .dcd file or .coor file

Date: Thu Mar 18 2010 - 07:29:55 CDT

Hi Rabab,

to delete water molecules I use the tool catdcd combined with an
indexfile containing all atoms for your 'new' .dcd file. The indexfile
could be constructed with a vmd script.

Best regards,

Quoting Rabab Toubar <>:

> Hi all,
> I have searched the mailing list and there are lots of suggestions
> to totally remove the waters from a .dcd file after its generation.
> I was wondering if there is a way to remove some of the waters
> (specified by angstroms or solvation shells) to be removed so as to
> downsize the solvation box.
> Any suggestions?
> Thanks
> Rabab Toubar

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