AMBER Archive (2001)

Subject: water cap

From: Guanglei Cui (cuigl_at_morita.chem.sunysb.edu)
Date: Tue Jul 24 2001 - 23:29:45 CDT

Dear Amber Users,
   Recently I'm trying to pick up the solvatecap command and add a small
water cap to my system. In a few attempts, the water cap departed from
the system substantially even though all water molecules were still
capped with the specified sphere. What I see is that my system of
interest is in one place but the water cap is in another. To me, it
seems it is the cap that moved not the system itself. Could anyone show
me how to perform MD with water caps correctly? (I simply solvatecap mol
WATBOX216 {atom1 atom2 atom3} 12.5A and used default ivcap and fcap or
stronger fcap) Thanks in advance.

Regards,

Guanglei Cui
SUNY at Stony Brook