AMBER Archive (2000)

Subject: Re: problems in sander

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Sun May 07 2000 - 03:54:57 CDT

Better to use leap or cion to place ions electrostatically,
I think. Minimization will most likely have no effect on ion
placement except relieving steric contacts - long dynamics is
necessary and in any case cations will pair up with pairs of
waters (forming a ion-OW-ion-OW- box).

For the abrupt warming problem, you should include your mdin file.

Bill Ross