Are you using a non-orthorhombic box by chance? The QM region check assumes
this, so sometimes it gives an error when there actually isn't one
(especially with triclinic boxes).
Also, have you visualized the trajectory to make sure the QM region
actually isn't too big? Up until a few bug fixes ago the QM code would
occasionally not SCF converge and cause "explosions". Frequently the first
check that bombed out because of this was the QM region/box check.
Restarting with a different random seed would almost always made this go
away, although I haven't seen this since the bug fix.
Regards,
Brian
On Thu, Mar 14, 2013 at 10:42 AM, R. Xiong <rchxiong.gmail.com> wrote:
> I am running QM/MM simulations using Amber with iwrap=1. It was running
> successfully, but when I restart the program, the program crashes because
> of QM/MM region is too large. I believe this should be caused by iwrap
> option. If iwrap=0, this problem will disappear, but my question is that if
> there is any way to deal with the problem when still using iwrap=1.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 14 2013 - 09:30:03 PDT
