AMBER Archive (2004)

Subject: AMBER: Box range in vacuum when restart MD

From: scopio (
Date: Wed Jun 23 2004 - 08:22:31 CDT

Dear Amber Users:

I'm now doing MD in vacuum using Amber7 on my protein which contains
about 20,000 atoms. I first equilibrate it in a stage of 0K to 300K for
100ps. Then, I want to do second equilibration for another 100ps. I want
to let Sander read X and V informatin via ntx=7. But I got error
messages as follows:
 parameter alpha: (unit cell angle) has value -0.97091E+00
 This is outside the legal range
 Lower limit: 0.30000E+02 Upper limit: 0.15000E+03
 Check ew_legal.h

While use ntx=5 is OK.

I searched in the archive. ntx=7 will read X, V as well as Box whereas
ntx=5 don't read Box. So it's obvious that the Box information read in
by sander from rst file is beyond 30A. But how could this happen? I
checked the trajectory, it looks fine and no strange things could be
found. Any helps? Thanks in advance!

Best Regards!

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