VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Mon Oct 02 2000 - 00:22:25 CDT

David,

Since you're using NAMD, I assume you had some way of generating psf files,
i.e. either charmm or xplor? Either of these programs would be able to
modify the structure file to include, say, just the protein.

You could probably do what you want with VMD, but it would be rather
laborious. Briefly, you could create an atom selection in the text
console containing only the atoms you want, then write pdb files for
each time step in the trajectory. After loading each pdb back into VMD,
you could have VMD write the frames back out as a DCD file.

Justin

 
On Mon, Oct 02, 2000 at 01:47:14PM +1000, David Chalmers wrote:
> Hi all,
>
> I have been using NAMD to do some dynamics of a protein in a water box. I
> am currently looking for ways to analyse the output dcd file. I have a
> few questions.
>
> 1. What programs are people using to analyse their dynamics data?
>
> 2. Can I use VMD to, for example, delete the water molecules from my
> dynamics trajectory? This would reduce the size of the input file so that
> I could look at the trajectory without my SGI swapping so much!
>
> 3. Does anybody have a conversion utility to convert dcd files in to
> other formats?
>
> Thanks for any help you can offer.
>
> David
> _____________________________________________________________________________
>
> David Chalmers Lab: 9903 9110
> Victorian College of Pharmacy Fax: 9903 9582
> 381 Royal Pde, Parkville, Vic 3053 http://synapse.vcp.monash.edu.au
> Australia David.Chalmers_at_vcp.monash.edu.au
> _____________________________________________________________________________
> 

-- 
Justin Gullingsrud      3111 Beckman Institute
H: (217) 384-4220       I got a million ideas that I ain't even rocked yet...
W: (217) 244-8946       -- Mike D