Re: amber-developers: Extra Points Calculation

From: Robert Duke <>
Date: Wed, 12 Nov 2008 10:15:44 -0500

Oh, sorry. I missed that TI was involved. So I guess you all have to
figure out whether this is a disallowed combination in sander. I am open to
doing TI at some point in pmemd, if I can figure out a way to actually get
decent performance (as I best recall from the last Sannibel, we discussed
this, I looked at the issues involved with the new TI, and found some stuff
that was problematic from a performance perspective).
Regards - Bob

----- Original Message -----
From: "David A. Case" <>
To: <>
Sent: Wednesday, November 12, 2008 9:21 AM
Subject: Re: amber-developers: Extra Points Calculation

> On Wed, Nov 12, 2008, Robert Duke wrote:
>> Multiple processor minimization is very standard; if it does not work, it
>> is a bug!!!
> True, but note that Ilyas' problem is with minimization coupled to
> thermodynamic integration, i.e. minimzation on a "mixed" potential
> surface.
> So this would not arise in pmemd, (although I am still hopeful that
> sometime
> I can convince you that putting TI into pmemd is a worthy goal!)
> Volodymyr has pointed out updates that may fix Ilyas' problem. I'm hoping
> that this does the trick.
> ...dac
Received on Fri Dec 05 2008 - 14:33:47 PST
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