Re: [AMBER] Watercap... some querries

From: David A. Case <case.biomaps.rutgers.edu>
Date: Wed, 28 Jan 2009 10:01:46 -0500

On Wed, Jan 28, 2009, Waqas Nasir wrote:
>
> 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?

I don't think sander/pmemd support multiple caps ... there is just one.

>
> Moreover,
> when igb=10 with watercap enabled, does that mean that the atoms
> outside the cap are in the implicit solvent simulation

Yes.

...dac


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 30 2009 - 01:27:06 PST
Custom Search