From: Chris Harrison (charris5_at_gmail.com)
Date: Mon Aug 17 2009 - 09:44:35 CDT
Yoaz,
Any errors or issues introduced to the psf prior to ionization would be
propogated and not expected to be fixed during creation of the ionized psf.
I would recommend attempting short test simulations (in vacuum) of your
various psfs from the stages leading up to ionization to isolate at what
stage the error was introduced. This will narrow the focus, helping you to
identifiy the source of the problem.
Chris
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078 On Mon, Aug 17, 2009 at 5:04 AM, Yoav Beck <ucbpybe_at_ucl.ac.uk> wrote: > Dear Yingzhe, > > If that's the problem then I have no idea how to track down those errors. > The psf file I am using was made during ionization and I did inspect it, but > couldn't find anything peculiar. > > Cheers. > > Yoav. > > yzliu wrote: > >> Dear Yoav, >> I have met the error because there are some mistakes on the my psf of >> water. >> best wishes, >> yingzhe >> >> 2009/8/13 Yoav Beck <ucbpybe_at_ucl.ac.uk <mailto:ucbpybe_at_ucl.ac.uk>> >> >> >> Dear all, >> >> When running md or minimization on my membrane protein complex on >> more than one processor (it seems to work fine with only one >> processor) I get this: >> >> Info: Entering startup at 35.8069 s, 14.2221 MB of memory in use >> Info: Startup phase 0 took 0.052151 s, 14.2222 MB of memory in use >> FATAL ERROR: Tried to find atom type on node other than node 0 >> ------------- Processor 8 Exiting: Called CmiAbort ------------ >> Reason: FATAL ERROR: Tried to find atom type on node other than node 0 >> >> FATAL ERROR: Tried to find atom type on node other than node 0 >> ------------- Processor 9 Exiting: Called CmiAbort ------------ >> Reason: FATAL ERROR: Tried to find atom type on node other than node 0 >> >> [8] Stack Traceback: >> [0] CmiAbort+0x5f [0xa4b62f] >> [1] _Z8NAMD_diePKc+0x62 [0x4ffe02] >> [2] _ZN8Molecule17build_atom_statusEv+0x1629 [0x88a8a5] >> [3] _ZN8Molecule16receive_MoleculeEP8MIStream+0xdb3 [0x88380d] >> [4] _ZN4Node11namdOneRecvEv+0x4b7 [0x8a0907] >> [5] _ZN4Node7startupEv+0xebe [0x89fcba] >> [6] _ZN12CkIndex_Node18_call_startup_voidEPvP4Node+0x12 [0x89edf8] >> [7] CkDeliverMessageFree+0x21 [0x9c2af1] >> [8] _Z15_processHandlerPvP11CkCoreState+0x509 [0x9c20e5] >> [9] Stack Traceback: >> [0] CmiAbort+0x5f [0xa4b62f] >> [1] _Z8NAMD_diePKc+0x62 [0x4ffe02] >> [2] _ZN8Molecule17build_atom_statusEv+0x1629 [0x88a8a5] >> [3] _ZN8Molecule16receive_MoleculeEP8MIStream+0xdb3 [0x88380d] >> [4] _ZN4Node11namdOneRecvEv+0x4b7 [0x8a0907] >> [5] _ZN4Node7startupEv+0xebe [0x89fcba] >> [6] _ZN12CkIndex_Node18_call_startup_voidEPvP4Node+0x12 [0x89edf8] >> [7] CkDeliverMessageFree+0x21 [0x9c2af1] >> [8] _Z15_processHandlerPvP11CkCoreState+0x509 [0x9c20e5] >> FATAL ERROR: Tried to find atom type on node other than node 0 >> ------------- Processor 2 Exiting: Called CmiAbort ------------ >> Reason: FATAL ERROR: Tried to find atom type on node other than node 0 >> >> FATAL ERROR: Tried to find atom type on node other than node 0 >> ------------- Processor 3 Exiting: Called CmiAbort ------------ >> Reason: FATAL ERROR: Tried to find atom type on node other than node 0 >> >> [9] CsdScheduleForever+0xa5 [0xa4c42d] >> >> I checked the mailing and saw people with similar problems but no >> answer. I am using 2.7b1 on a linux cluster. >> >> Any help or insight will be greatly appreciate. >> >> Thanks. >> >> Yoav. >> >> >> >> >> -- >> ============================== >> Yingzhe Liu >> PHD Student of Analytical Chemistry >> Chemistry Department >> Nankai University >> Tianjin, P.R.China,30071 >> Email: nk.liuyz_at_gmail.com <mailto:nk.liuyz_at_gmail.com> >> ============================== >> > >
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