AMBER Archive (2006)

Subject: Re: AMBER: Question about using PMEMD and GB

From: H W (howardww_at_gmail.com)
Date: Wed Sep 06 2006 - 13:31:20 CDT

Thank you, Dr. Case.

--Howard

On 9/6/06, David A. Case <case_at_scripps.edu> wrote:
> On Wed, Sep 06, 2006, H W wrote:
> >
> > I want to use PMEMD and GB to simulate a protein, with flag igb=2.
> > Should I set ntb=0? On the manual it says "no periodicity is applied
> > and PME is off. But I want to use PME+GB to do the simulation.
>
> You can't do that: there is no way to use PME with GB.
>
> >
> > Another question is, do I need to add counter ions to the system? When
> > I add counter ions, say two Na+, they just go away and cause restart
> > file crash.
>
> The straightforward advice is: don't use counterions; set saltcon instead.
> Basically, if you are willing to give up an atomic description of the water
> molecules, you should probably be prepared to give up an atomic description
> of the counter-ions as well.
>
> You don't need to follow this advice, of course. But be aware that such
> calculations would represent a research effort into simulation methodology,
> and almost certainly would require modifications to the code and a lot of
> testing.
>
> ...dac
>
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