AMBER Archive (2007)Subject: RE: AMBER: box size bomb in QMMM calculation
From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jun 12 2007 - 22:39:35 CDT
Hi Bud,
> > cut off unreasonably small for this, say 0.1 A just to
> force it to get to
> > the pdb writing stage.
> >
>
> That was my plan, but it never gets far enough to do that. It bombs
> before the QM region pdb write occurs.
Did you try setting cut=0.1? That should get you through to the pdb writing
phase, although obviously the actual MD will be garbage. Alternatively you
could try turning off periodic boundaries - set ntb=0, then it will skip the
cut off bounding check and you;ll get a pdb.
> Unfortunately, I'm leaving tomorrow morning to go to the US
> Grand Prix.
Wow, lucky for some... I just have to resign myself to watching it on Speed.
Enjoy...
All the best
Ross
/\
\/
|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
|