AMBER Archive (2003)

Subject: Re: diffusion coefficients

From: David A. Case (case_at_scripps.edu)
Date: Mon Apr 14 2003 - 01:03:15 CDT

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_at_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
==================================================================