AMBER Archive (2007)

Subject: RE: AMBER: follow-up

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Oct 09 2007 - 16:24:50 CDT

Hi Wenyong,

> My g.ann.rst file has " ****" as follows:
>
> 2153.6966097************5332.72304812153.4352331************53
31.5924867
> 2152.8627430************5331.94715012154.7117253************53
31.0164644
> .......
> ************************************7816.6234070**************
**********
> 0.0035586 0.0233672 -0.0140135 -0.0294524
> 0.0219386 0.0164750
> .....
>
> What are problems here?

You have solvent molecules that have diffused too far. Take your last good
restart file and run 1 step with iwrap=1 and it will wrap everything into
the central image. Then you can either proceed with iwrap=1 to always wrap
or just continue running until your waters diffuse too far again.

Good luck,

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