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_slab_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 - 02:00:02 PDT
