Hello AMBER
I have installed AMBER 8 on a new system. When I run sander the output
prints out to where it list the SIZE OF NONBOND LIST. At this point, I
can wait for an hour and nothing happens although sander is still
running. My worry is that my protein system with waters may be too
large. I have over 200,000 atoms with 54169900 nonbonded contacts. Would
a stalling at this point in the log be symptomatic of too large a
system? If so, I can compile AMBER to accept larger systems?
Thanks,
Steve
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Received on Wed Apr 08 2009 - 01:10:04 PDT
