AMBER Archive (2009)

Subject: Re: [AMBER] pmemd and internal dielectric

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Fri Sep 25 2009 - 11:44:56 CDT

My personal view on this is that one SHOULD not change intdiel or
extdiel in gb, and doing so might be harmful to your health.

The gb parameters are fitted in various ways to reproduce PB results in
WATER, using 1 and 80 for the dielectrics.

While the program allows you to specify those terms separately, the
answers you will get are surely wrong.

How wrong ? not sure, I do not think anyone really tested it, and we
would wellcome someone trying.

 From a formal point of view, do not change them !

Adrian

Robert Duke 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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-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
                             Quantum Theory Project
                            Department of Chemistry

                  Senior Editor. Journal of Physical Chemistry
                           American Chemical Society

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu

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