AMBER Archive (2009)

Subject: Re: [AMBER] pmemd and internal dielectric

From: Robert Duke (rduke_at_email.unc.edu)
Date: Fri Sep 25 2009 - 15:10:57 CDT

Hi Serguei,
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, and update the code in amber 11 to not allow changes to this in pmemd
11, unless there are complaints (ie., amber 11 pmemd will issue a warning
and force intdiel to the default value). I am taking this approach since 1)
pmemd is supposed to be primarily "production" code as opposed to
experimental code, and 2) there would be a (very) slight performance impact
in the dihedral code (we are probably talking barely measureable). Thanks
very much for reporting this though, and sorry for the hassles.
Best Regards - Bob Duke

----- Original Message -----
From: "Serguei Vassiliev" <svassiliev1_at_gmail.com>
To: <AMBER_at_ambermd.org>
Sent: Friday, September 25, 2009 3:47 PM
Subject: Re: [AMBER] pmemd and internal dielectric

> Hi Bob,
> Well, I'm not too desperate, I can do computations with sander for now.
> I
> just got confused yesterday by discrepancies in EEL between
> sander/pmemd/namd untill I figured out what was going on, and thought I
> should let you know about this problem.
>
> All the best
> Serguei
>
>
>
> On 9/25/09, Robert Duke <rduke_at_email.unc.edu> wrote:
>>
>> Hi Serguei,
>> Well, you are absolutely right. Somehow when doing the gb port to pmemd,
>> I
>> missed the fact that there were mods out in the default dihedral code.
>> The
>> use of nonstandard intdiel is something we obviously don't test for (and
>> since the default is 1.0, then we obviously would miss it in standard
>> testing). How desperately do you want this "right now"? Can anyone in
>> the
>> gb community comment on the wisdom of dinking with the intdiel parameter?
>> Best Regards - Bob Duke
>> ----- Original Message ----- From: "Serguei Vassiliev" <
>> svassiliev1_at_gmail.com>
>> To: <amber_at_ambermd.org>
>> Sent: Friday, September 25, 2009 11:47 AM
>> Subject: [AMBER] pmemd and internal dielectric
>>
>>
>> Dear all,
>>>
>>> I am doing GB calculations with sander and pmemd. When intdiel = 2.0
>>> sander
>>> scales both EEL and EEL1-4 energy terms, while pmemd appears to scale
>>> only
>>> EEL. Could anybody comment on this? It look to me like a bug in pmemd.
>>>
>>> Thanks,
>>>
>>> Sergey
>>> _______________________________________________
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>>>
>>>
>>>
>>
>>
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