AMBER Archive (2008)

Subject: Re: AMBER: query about Generalized Born simulation

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Apr 11 2008 - 09:15:53 CDT

no, PME cannot be used with a GB simulation in Amber.

On Fri, Apr 11, 2008 at 9:42 AM, <gurvisha_at_leadinvent.com> wrote:

>
> Dear Amber users
>
> I am trying to run an implicit GB simulation for protein-DNA complex using
> amber9. My doubt is whether PME can be turned on for an implicit GB
> simulation. Although the Amber9 manual states that Generalized Born
> simulations can only be run for non-periodic systems, i.e. where ntb=0, it
> also mentions that the nonbonded cutoff for GB calculations should be
> greater than that for PME calculations. So can PME be used for a GB
> simulation?
>
>
> Regards
> Gurvisha Sehgal
>
> LeadInvent Technologies
> Technology Business Incubation Unit(TBIU)
> IIT Delhi
> Hauz Khas, New Delhi 110 016
> INDIA.
>
>
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