From: Werner Crous (crous.werner_at_gmail.com)
Date: Sat Mar 13 2010 - 10:22:47 CST

Dear NAMD-users

I setup a large system in CHARMM, done minimization and 200ps NPT dynamics,
with no problems. However, when I tried to continue dynamics with NVT in
NAMD I got the error listed in the subject line. I read almost every account
of this error on the list, and it seems to me that it has to do with the way
in which NAMD partitions the system in patches and that some of the water
molecules in my system, that were wrapped to the unit cell by NAMD, were
"split" in the process with some atoms of the water molecules at the top and
others at the bottom of the unit cell. As I understand it, NAMD cannot put
molecules with "elongated bonds " longer than the cut-off distance in a
patch and this causes the error. I do not understand how this could have
happened since I imaged my water molecules in CHARMM by residue. Can someone
please tell me if there is a quick way of fixing this and how to prevent
this error form occurring in the future? I ran successful simulations with
NAMD in the past and this is the first time this error occurs.

Best regards

Werner Crous
Scientific Computing Research Unit
University of Cape Town
Rondebosch 7701
South Africa
Phone: +27 21 650 2530 (O)
Fax: +27 21 686 4333

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