Dan,
pmemd.MPI gave me SHAKE error at the very start, the parallel job crashed immediately. Serial pmemd did not have this problem at all. It's running, I'm pretty sure it will finish in the end.
If the structure was not sufficiently minimized, I don't understand why serial pmemd worked just fine with and without SHAKE... It feels like there may be some bug in pmemd.MPI.
DX
________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
To: Danny Xu <quantum_mania.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Wednesday, August 17, 2011 10:20 PM
Subject: Re: [AMBER] Coordinate resetting cannot be accomplished, deviation is too large
Quick question - when you say serial pmemd works fine, do you mean it
completes all 850000 steps? Is it able to complete more steps than the
parallel run? Usually when you receive a message like this:
On Wed, Aug 17, 2011 at 10:13 PM, Danny Xu <quantum_mania.yahoo.com> wrote:
> Coordinate resetting cannot be accomplished,
> deviation is too large
and see behavior like this:
> If I disable SHAKE (ntc=1, ntf=1), pmemd.MPI job will run, but energies blow up in a short period of time.
it means your starting coordinates are not well-minimized.
-Dan
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Received on Wed Aug 17 2011 - 22:30:02 PDT
