Hello,
Yes, such features would be greatly appreciated.
Best regards,
JM
----- Original Message -----
From: José Guilherme Vilhena Albuquerque d'Orey
Sent: 05/16/13 09:44 AM
To: amber.ambermd.org
Subject: [AMBER] SMD pulling GPU
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 ==================================================== _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 16 2013 - 04:00:02 PDT
