VMD-L Mailing List

From: David Chalmers (david.chalmers_at_vcp.monash.edu.au)
Date: Sun Oct 01 2000 - 22:47:14 CDT

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
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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
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