Re: [AMBER] transition metal system works on pmemd crashes on pmemd.cuda

From: Jason Swails <>
Date: Wed, 22 Aug 2012 10:50:05 -0400

On Wed, Aug 22, 2012 at 10:28 AM, Patrick von Glehn <> wrote:

> Hi Scott,
> Thanks for your reply.
> Do you have reason to believe that the new patch will resolve this
> error? Were you able to reproduce the error with an unpatched version
> of amber? Also, forgive my ignorance, but what does TOT mean?

Top Of Tree, I think :). What this means is that he doesn't see the error
with the soon-to-be-released pmemd.cuda upgrade (I don't think the current
version of amber was tested, but the upcoming patch is known to have fixed
a handful of bugs).

> What sort of timescale are we talking about here for the new patch
> release? Days/weeks/months? I am very keen to get my GPU simulations
> going!

No promises here, but in conversations I've had with Ross, I would say
we're aiming for 'days'. The patch is a large one, and has to be handled
with care, but we're taking a crack at generating the patch tonight. If
the merge goes smoothly and everything tests out correctly the first time
through, you probably will not have more than a few days to wait.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Wed Aug 22 2012 - 08:00:04 PDT
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