AMBER Archive (2008)

Subject: Re: AMBER: STEERED MD

From: Robert Duke (rduke_at_email.unc.edu)
Date: Fri May 16 2008 - 12:29:29 CDT

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

----- 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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