From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Mar 28 2006 - 14:31:59 CST
Hi Lily,
it is correct that psfgen uses only the topology file, and namd uses
only the parameter file. This is because the topology file contains the
information necessary to /build /the molecule (charges, connectivities,
and such), but the paramter file contains the information for
simulations (bond strengths and such). Please see the secion on top and
par files in the namd tutorial for more information:
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node22.html
Peter
lily jin wrote:
> I can generate the topology file now for PO3, but not the parameter
> file. But it seems that psfgen dose not use para file, dose it? How
> dose psfgen use the para file? How dose NAMD use the para file? Thank you!
>
>
> *Lily*
>
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