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Department of Chemistry and Chemical Biology |
Questions and problems?SanderCould you show me how to increase the "Max Npairs" for the parallel version of sander? I have a large protein system. It works fine with the non-parallel version, but crashes when running the parallel version given the following message:Npairs = 1554372 Exceeds Max= 1250000 The parallel version and some serial versions are statically dimensioned. Change MAXPR in sizes.h and recompile. Does anyone know what the size of the parameters ... for 90,000 atoms If you aren't running a parallel version, it is likely these are decided automatically (i.e. if -DMEM_ALLOC is in MACHINEFLAGS in the MACHINE file). Thus, if you are running parallel & you can get a serial version compiled w/ MEM_ALLOC, you can run a step and see what size things get dimensioned to & update your (statically dimensioned) parallel version. The wild card will be MAXPR (# of pairs) since this can increase as the system densifies on equilibration. Web Masters <webadmin@www.amber.ucsf.edu> Last modified: Fri Jul 25 12:19:55 PDT 1997 |
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