Hi,
To answer your first question: Delphi can't be run on more than one
processor. It can be made quasi-parallel by sending each snapshot to its own
processor and I believe the mm_pbsa.pl released in amber11 should have this
capability.
On Tue, Jun 1, 2010 at 3:55 PM, Yuqin Cai <yuqin.cai.2008.gmail.com> wrote:
> Dear AMBER community,
>
> I am computing free energies for three carcinogen-containing duplexes using
> MM-PBSA. By replacing the carcinogen with a hydrogen atom, i can compare
> the
> distortion each carcinogen causes to the B-DNA duplex. Here are my
> questions:
>
> 1) how to use multiple processes, especially during delphi? For an 800
> atom
> structure, it took me ~2 weeks to get the average free energy over 5000
> snapshots. I wonder if i could make it faster.
>
> 2) how to put out the results for each snapshot during the trajectory,
> instead of an overall average, so that I can do a clustering analyses?
>
> 3) how to cap the ends if i want to carry out analyses for a cropped
> structure?
>
> Many thanks,
>
> Yuqin
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>
--
T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Tue Jun 01 2010 - 13:30:04 PDT
