AMBER Archive (2009)

Subject: Re: [AMBER] pmemd and internal dielectric

From: Robert Duke (rduke_at_email.unc.edu)
Date: Fri Sep 25 2009 - 11:07:06 CDT

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

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