Dear Andrew,
You cannot use PME in an non-periodic system in sander.
Thus you must turn off PME or use the gb method.
for a non-periodic, with PME turned off, you would need
to set:
&ewald
use_pme=0, vdwmeth=0, eedmeth=4,
&end
The other way is to set igb=2 in the &cntrl namelist.
The error you are seeing is from the pme method
trying to figure out how to split up your
unit cell which does not exist in a vacuum simulation.
I will see about a better error message.
Best wishes,
Mike
From Ryan.H.Lilien_at_Dartmouth.EDU 31 Oct 2000 13:38:04 EST
Message-id: <36523709.dasher.Dartmouth.EDU>
Date: 31 Oct 2000 13:38:04 EST
From: Ryan H. Lilien <Ryan.H.Lilien_at_Dartmouth.EDU>
To: AMBER list <amber.heimdal.compchem.ucsf.edu>
Subject: file format question
In-Reply-to: <PME>
Hello,
I'm looking at the all-atom n-terminal amino acid residues file "
http://amber.ch.ic.ac.uk/ff94/all_aminont94.in" and can't seem to find a description of the file format used there. Could you please point me towards a description of these .in files?
Thanks,
Ryan Lilien
--------------------
Department of Computer Science
Dartmouth College
Hanover, NH 03755
USA
Received on Tue Oct 31 2000 - 10:03:42 PST
