AMBER Archive (2009)

Subject: [AMBER] Watercap... some querries

From: Waqas Nasir (nasirwaqas1983_at_yahoo.com)
Date: Wed Jan 28 2009 - 08:54:00 CST

Hi,

Hope every one is doing fine.

Well, just wanted to
ask if I use multiple "solvatecap" commands for the explicit solvent,
will it have any negative effect on the simulation... I mean does the "overall"
cap need to be spherical always or we can use multiple solvatecap
commands to cover irregular portions of the system and hence generate
an overall irregular shaped water covered area. Or may be using a
larger cap with the center deeper into the protein is recommended?

Moreover,
when igb=10 with watercap enabled, does that mean that the atoms
outside the cap are in the implicit solvent simulation (beause of the
default values in &pb naming list). I am a bit confused here.

Any comments are highly appreciated.
Thanks,
Waqas.

      
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber