Hi Guilherme,
No COM is not supported on the GPU in AMBER 12. The fact the code did not
quit is considered a bug. Please update your AMBER 12 tree and it will
correctly quit with an error message if you try to run with COM restraints.
Note calculating the center of mass of a large group of atoms is a
difficult problem ultimately requiring a reduction in parallel. Hence
using such restraints (even in the CPU code) will unfortunately lead to a
reduction in efficiency.
All the best
Ross
On 5/16/13 1:44 AM, "José Guilherme Vilhena Albuquerque d'Orey"
<guilhermevilhena.gmail.com> wrote:
>Dear Sir/Madam,
>
>I was wondering if the COM steered MD is already available for the
>pmemd.cuda in amber12. I have tried it but it doesn't give me any error
>nor
>it makes what it should.
>Furthermore how can I increase the number of residues that belong to the
>COM (sander or pmemd). I need to pull a whole protein up (~ 1200
>residues),
>and apparently there is some kind of maximal limit to the string I can
>use
>to define the COM. I have tried to change that variable inside AMBER
>(pmemd)
>nmr_calls.F90: integer maxigr
>The default is 200. I have tried to increase to 500 and it is still not
>working. The error that is outputted is what follows.
>Note that decreasing the number of residues in the COM it works.
>
>
>pmemd.MPI:12508 terminated with signal 11 at PC=579d27 SP=7fff988ba9d0.
> Backtrace:
>/home/gvilhena/CODES/amber12_MOD/bin/pmemd.MPI(pme_slab_recip_mod_mp_fill_
>charge_grid_+0x937)[0x579d27]
>/home/gvilhena/CODES/amber12_MOD/bin/pmemd.MPI(pme_slab_recip_mod_mp_do_sl
>ab_pmesh_kspace_+0x14d4)[0x5790e4]
>/home/gvilhena/CODES/amber12_MOD/bin/pmemd.MPI(pme_force_mod_mp_pme_force_
>+0x2d56)[0x562796]
>/home/gvilhena/CODES/amber12_MOD/bin/pmemd.MPI(runmd_mod_mp_runmd_+0x1382)
>[0x552932]
>/home/gvilhena/CODES/amber12_MOD/bin/pmemd.MPI(MAIN__+0x808)[0x4eed78]
>/home/gvilhena/CODES/amber12_MOD/bin/pmemd.MPI(main+0x3c)[0x41dd6c]
>/lib64/libc.so.6(__libc_start_main+0xf4)[0x3bf881d994]
>/home/gvilhena/CODES/amber12_MOD/bin/pmemd.MPI[0x41dc79]
>
>
>Thanks in advance!
>All the best,
>Guilherme Vilhena
>
>--
>====================================================
>*Guilherme Vilhena, Ph.D*
>
>Universidad Autonoma de Madrid,
>Departamento de Fisica Teorica de la Materia Condensada
>Facultad de Ciencias, Modulo C-5
>E-28049 Madrid, Spain
>
>tel: +34 91 497 2789
>fax: +34-91-4974950
>====================================================
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Received on Thu May 16 2013 - 08:00:02 PDT
