On Sun, Apr 13, 2003, yuan bo wrote:
> I am simulating protein in mixed solents and saved
> trajectory in every 0.2ps for analysis. now I want to
> calculate diffusion coefficients of solvent for one
> 100ps trajectory ( 500=100/0.2 sets data, using Ptraj
> program in Amber 6. Manual define diffusion as
> follows:
> diffusion mask time_per_frame [ average ] [
> filenameroot ]
> The time_per_frame sepicifies time between frams in
> ps. I use " diffusion :WAT 4 average filename" command
If the time between your snapshots (frames) is 0.2 ps, why did you
put "4" in your command for time_per_frame? I think that number should
be 0.2.
...hope this helps...dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Mon Apr 14 2003 - 07:53:01 PDT
