Hi Dave,
I understand your concern. I'll try to get a patch out sometime next
week. - Bob
----- Original Message -----
From: "case" <case.biomaps.rutgers.edu>
To: "AMBER Mailing List" <amber.ambermd.org>
Cc: <onufriev.cs.vt.edu>
Sent: Friday, September 25, 2009 5:59 PM
Subject: Re: [AMBER] pmemd and internal dielectric
> 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
>
>
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Received on Fri Sep 25 2009 - 15:30:04 PDT
