AMBER Archive (2009)

Subject: [AMBER] Sander Stalling

From: Steve Seibold (
Date: Mon Apr 06 2009 - 11:21:51 CDT



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?






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