Re: diffusion coefficients

From: David A. Case <case.scripps.edu>
Date: Sun, 13 Apr 2003 23:03:15 -0700

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

-- 
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David A. Case                     |  e-mail:      case.scripps.edu
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Received on Mon Apr 14 2003 - 07:53:01 PDT
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