Catherine:
My experience has been that sander and PMEMD yield essentially the same
results as NAMD. I haven't directly compared trajectories from each program,
but DNA helical parameters that I calculate are the same, within the limits
of sampling. AMBER and NAMD use the same integration algorithms, I believe.
(Correct me if I'm wrong!)
Why not just use NAMD, though?
Cheers,
Robert Elder
PhD Candidate -- University of Colorado-Boulder
2010/5/24 Catein Catherine <askamber23.hotmail.com>
>
> Dear Sir/Madam,
>
>
>
> Did any one compared the MD trajectory or binding energy results obtained
> by NAMD or AMBER's sander or pnemed? I am trying to reproduce the results
> of NAMD reported in literature, should I use sander or pnemed? I wonder if
> similar aligorithems are used in NAMD and Sander/Pnemed?
>
>
>
> Best regards and many thanks for your advices,
>
> Catherine.
>
>
>
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Received on Mon May 24 2010 - 13:00:03 PDT
