AMBER Archive (2004)

Subject: Re: AMBER: MD & net charge

From: bybaker_at_itsa.ucsf.edu
Date: Mon Aug 30 2004 - 17:02:53 CDT

('binary' encoding is not supported, stored as-is) Thank you very much for the suggestion.

I will try both and see what the differences are.

All the best.

Bo

On Mon, 30 Aug 2004 16:57:50 -0400 Carlos Simmerling wrote:

> you can get just the force field files from
> http://amber.scripps.edu/dbase.html
>
> whether you should allow PME to use a neutralizing plasma or add
> counterions
> doesn't have a definite answer (yet). some people argue for each approach.
> ions are more accurate in principle but take time to equilibrate, and
> without
> equilibration they may be worse than not having them at all. it's really
> an area of
> current research.
>
> bybaker_at_itsa.ucsf.edu wrote:
>
> >Thanks for the advice.
> >
> >Since we only have Amber7 available, I might have to use the old parm94.
> >
> >Do I still need to neutralize the entire system before subject to MD?
> >
> >Thank you.
> >
> >Bo

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