Yes I plan to. I am testing it. Along with juggling a bunch of other
stuff...
> -----Original Message-----
> From: peker milas [mailto:pekermilas.gmail.com]
> Sent: Monday, January 03, 2011 7:40 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] calculations failed on GPU with ntr=1 (with bugfix 11
> applied)
>
> Dear amber users/coders,
>
> I am having a similar problem with my GPU. I would like to ask if we
> will have this new bug fix today.
>
> thank you so much
>
> peker milas
>
> On Sun, Jan 2, 2011 at 12:17 PM, Ross Walker <ross.rosswalker.co.uk>
> wrote:
> > Hi Dmitry,
> >
> > This problem is known, it is caused by the 10 angstrom cutoff with a
> relatively small box size. If you set your first simulations cutoff to 8
angstroms
> it should work fine.
> >
> > A bugfix addressing this problem and some other minor issues will be
> released on Monday. Stay tuned.
> >
> > All the best
> > Ross
> >
> >> -----Original Message-----
> >> From: Dmitry Mukha [mailto:dvmukha.gmail.com]
> >> Sent: Sunday, January 02, 2011 6:12 AM
> >> To: AMBER Mailing List
> >> Subject: [AMBER] calculations failed on GPU with ntr=1 (with bugfix 11
> >> applied)
> >>
> >> Amber 11 pmemd.cuda fails to get a meaningful results with the
following
> >> input, but with the second one works fine. All available bugfixes
including
> >> 11th were applied. The output files are attached to the mail.
Surprisingly,
> >> all steps were completed, but with NaN bond and huge angle energy
> values.
> >> Also coordinates became infinite.
> >>
> >> Stage 4 - density equilibration
> >> &cntrl
> >> imin=0,irest=1,ntx=5,
> >> nstlim=25000,dt=0.002,
> >> igb=0, ntc=2,ntf=2,ntp=1, taup=1,
> >> cut=10.0, ntb=2,
> >> ntpr=500, ntwx=500, ntwr=25000,
> >> iwrap=1,
> >> ioutfm=1, ig=75397747,
> >> ntt=3, gamma_ln=2.0, temp0=300.0,
> >> * ntr=1*,
> >> &end
> >> Restraints for PMEMD
> >> 2.0
> >> RES 1 1
> >> END
> >> END
> >>
> >> Stage 4 - density equilibration
> >> &cntrl
> >> imin=0,irest=1,ntx=5,
> >> nstlim=25000,dt=0.002,
> >> igb=0, ntc=2,ntf=2,ntp=1, taup=1,
> >> cut=10.0, ntb=2,
> >> ntpr=500, ntwx=500, ntwr=25000,
> >> iwrap=1,
> >> ioutfm=1, ig=75397747,
> >> ntt=3, gamma_ln=2.0, temp0=300.0,
> >> * ntr=0,*
> >> &end
> >> Restraints for PMEMD
> >> 2.0
> >> RES 1 1
> >> END
> >> END
> >> *
> >> $ uname -a*
> >> Linux 2.6.31.5-127.fc12.x86_64 #1 SMP Sat Nov 7 21:11:14 EST 2009
x86_64
> >> x86_64 x86_64 GNU/Linux
> >> *$ cudafe --version*
> >> cudafe: NVIDIA (R) Cuda Language Front End
> >> Portions Copyright (c) 2005-2010 NVIDIA Corporation
> >> Portions Copyright (c) 1998-2005 Edison Design Group Inc.
> >> Based on Edison Design Group C/C++ Front End, version 4.1 (Nov 3 2010
> >> 16:25:55)
> >> Cuda compilation tools, release 3.2, V0.2.1221
> >>
> >> --
> >> Sincerely,
> >> Dmitry Mukha
> >> Institute of Bioorganic Chemistry, NAS, Minsk, Belarus
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Mon Jan 03 2011 - 10:30:02 PST
