AMBER Archive (2003)

Subject: RE: AMBER: Simulation of small protein

From: Yong Duan (yduan_at_udel.edu)
Date: Thu Oct 23 2003 - 20:51:12 CDT

Dear Robert,

Equilibration at 100K should not require constraints.
Carlos probably knows his altered ff better :). But, without knowing the
detail, I'd hesitate to comment.
My favorite way is actually to watch the movie.
Aligning the simulated snapshots against the experimental structure is
another informative way.
After these, you then have to calculate the contacts, helicity, etc.

yong

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Endres, Robert G.
> Sent: Thursday, October 23, 2003 9:28 PM
> To: amber_at_scripps.edu
> Subject: RE: AMBER: Simulation of small protein
>
>
> Thanks, Yong and Carlos. Regarding the equilibration at 100K
> and the heating, do you do that with constraints? Also, how
> is the altered force field from the Carlos' Trpcage
> simulation? What's the best way to check what which helix
> does and to investigate the cause of the large RMSD? Many
> thanks again.
>
> -Robert
>

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