Re: [AMBER] MM_PBSA: multiple processes, single point output along the trajecotry and cropped structures

From: Dwight McGee <>
Date: Tue, 1 Jun 2010 16:21:19 -0400


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 released in amber11 should have this

On Tue, Jun 1, 2010 at 3:55 PM, Yuqin Cai <> 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
> _______________________________________________
> AMBER mailing list

T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
"Problems cannot be solved at the same level of awareness that created
               Albert Einstein
AMBER mailing list
Received on Tue Jun 01 2010 - 13:30:04 PDT
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