AMBER Archive (2008)

Subject: Re: AMBER: STEERED MD

From: fatima.chami_at_durham.ac.uk
Date: Sat May 17 2008 - 05:26:28 CDT

Quoting Robert Duke <rduke_at_email.unc.edu>:

>
> Okay, "minor" correction here. I DO support Jarzynski relation stuff in
> pmemd, ie. jar = 1. I think this falls under the perview of nmropt = 1, and
>
> probably is not particularly fast because there we use simpler
> communications protocols when a bunch of the nmr code is invoked (has to do
> with not touching some ancient code, basically). I was thinking of some
> stuff that came out of Rebecca Wade's group; that is actually supported
> only as a patch in earlier releases, though, so I don't know to what extent
> that would be considered "supported". Sorry for my confusion (I have heard
> steered MD used in different contexts).
> Regards - Bob Duke

Thanks for the feedback.
So the Jarzynski relation is implemented in PMEMD but not improved to run at
high parallel performance...so I better just use SANDER.MPI.

Another thing is that Umbrella sampling method necessites the use of the
weighted histogram to get free energy...I downloaded the WHAM utility program
but I have not used it yet ...
For the Steered MD...just using the Jarzynski relation will yield the free
energy..
am I getting things right here ...

regards
Fatima

>
> ----- Original Message -----
> From: "Robert Duke" <rduke_at_email.unc.edu>
> To: <amber_at_scripps.edu>
> Sent: Friday, May 16, 2008 1:15 PM
> Subject: Re: AMBER: STEERED MD
>
>
> > Sorry, no. Anything really fancy has three hurdles to pass: 1) are there
>
> > enough potential users, 2) is there actual potential to speed it up
> > (some things introduce requirements that basically run counter to good
> > performance), and 3) is it something interesting enough to the folks that
> > pay me that I can justify doing it. At least in the last round, this one
> > was not mentioned.
> > Regards - Bob Duke
> > ----- Original Message -----
> > From: <fatima.chami_at_durham.ac.uk>
> > To: <amber_at_scripps.edu>
> > Sent: Friday, May 16, 2008 12:25 PM
> > Subject: AMBER: STEERED MD
> >
> >
> >> Dear Amber users,
> >>
> >> does the PMEMD supports the steered MD calculation?
> >>
> >> best wishes
> >> Fatima
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>

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