AMBER Archive (2008)

Subject: Re: AMBER: query about Generalized Born simulation

From: rpaduri_at_chem.wayne.edu
Date: Fri Apr 11 2008 - 09:31:21 CDT

Hi,
I don't think you use PME with GB simulation. There are separate.
Sincerely
Raviprasad Aduri
Quoting gurvisha_at_leadinvent.com:

>
> 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.
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu