AMBER Archive (2008)

Subject: AMBER: imem keyword using mmpbsa

From: Sergio Wong (swong_at_mccammon.ucsd.edu)
Date: Thu Apr 03 2008 - 15:43:01 CDT

Dear Amber users;

     I'm running an mmpbsa calculation that includes the entropy
contribution via NMODE. Because my system is relatively large, I
occassionally run into memory allocation problems. To avoid this, I set
the NMODE input keyword imem = 1. That is, it would not compute eigen
vectors are computed. Since the mmpbsa.pl script creates an input
indicating nvect=0 (no eigen vectors should be calculated), I assume this
should yield the same results. Is this correct? Or does this change
somehow change the format of the output or in any other way change the
final entropy estimate?

Thanks;

-Sergio
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