Re: excluding water in dcd files

From: Jerry Ebalunode (jebalunode_at_UH.EDU)
Date: Mon Nov 03 2003 - 06:42:28 CST

What I normally do to this solve problem is to simply build an index file
decribing the indices for various atom entries in the pdb file using VMD in
your case protein atoms. This index file in combination with the CATDCD
program is then used to extract protein atom trajectories from the namd dcd
file. The output dcd file will contain trajectories of only the atoms that
you are interested in.

On Monday 03 November 2003 08:31 am, himanshu chandola wrote:
> dear namd users,
> is there any inbuilt functionality in namd wherein i have the
> option of whether the water molecules in my dcd files. This would make my
> work hell lot of easier because ultimately though i need to have the
> interaction of water molecules with my protein - i don't need to have
> their information stored in the dcd files .
> with kind regards,
> himanshu
> iit delhi
> ----------------------------------------
> Morpheus: Do you believe in fate, Neo?
> Neo: No.
> Morpheus: Why Not?
> Neo: Because I don't like the idea that I'm not in control of my life.

Jerry Ebalunode
Graduate Research Assistant
RM 402F Houston Science Center
Phone: 713-743-8367
Dept. of Biology and Biochemistry
University of Houston.
4800 Calhoun Road
Houston, TX 77204

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