AMBER Archive (2009)

Subject: Re: [AMBER] pmemd and internal dielectric

From: Serguei Vassiliev (svassiliev1_at_gmail.com)
Date: Fri Sep 25 2009 - 14:47:46 CDT

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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