AMBER Archive (2004)

Subject: AMBER: Aldo's PMEMD bug

From: Robert Duke (rduke_at_nc.rr.com)
Date: Mon Feb 09 2004 - 07:53:43 CST

Folks -
The problem Aldo turned up with PMEMD reading nmr restraints is really not a
restraints reading problem. Actually, the input specifies a nonperiodic
simulation (ntb=0) in combination with ewald (igb=0). This combination is
inconsistent, as ewald simulations require solvated systems with periodic
boundary conditions. The bug in pmemd 3.1 is that it does not catch the
ntb=0, and hangs somewhere while dealing with 0 box lengths and 0 box
angles. Bottom line on this is, if pmemd hangs on you, please be sure you
are using ntb>0 (pbc). This check has already been added for the amber 8
release.
Regards - Bob

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