AMBER Archive (2006)

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

From: David A. Case (case_at_scripps.edu)
Date: Wed Sep 06 2006 - 12:58:59 CDT

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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