AMBER Archive (2009)

Subject: Re: [AMBER] pmemd and internal dielectric

From: case (case_at_biomaps.rutgers.edu)
Date: Fri Sep 25 2009 - 16:59:56 CDT

On Fri, Sep 25, 2009, Robert Duke wrote:

> Okay, given the input from the GB developers (it is not a good idea to dink
> with this parameter), I am probably going to just leave amber 10 pmemd
> alone,

Hi Bob:

Could you easily create a patch (bugfix) that would just halt with an error
message saying "non-default intdiel is not supported" if intdiel is set to
something other than 1? I think we should do that rather than allow any
continued discrepancies between sander and pmemd.

As for Amber 11, I'm cc-ing to Alexey. His group has looked at these ideas,
and can comment on whether there is a legitimate need to enable this.
[Alexey: the question is whether there is a real need for non-default values
of intdiel in GB.]

> amber 11 pmemd will issue a
> warning and force intdiel to the default value

I think it's better to exit and force the user to manually change the input
file. It is too easy for warning messages to be overlooked, and this falls in
the "really bad" place where the results would be wrong but not obviously
wrong.

...thx...dac

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