AMBER Archive (2006)

Subject: Re: AMBER: Implicit solvent question

From: John Mongan (jmongan_at_mccammon.ucsd.edu)
Date: Fri Jun 23 2006 - 11:09:49 CDT

You can't, but you don't need to. Since implicit solvent simulations are
non-periodic, there is no problem with the system carrying a net charge.
The saltcon moderates the strength of electrostatic interactions (weaker
interactions with higher concentrations) -- it can't be used to
neutralize charge as counter-ions are in an explicit solvent simulation.

If you're planning to have two separate peptides in the same simulation,
  be aware that you may need to be careful to keep them together.
Non-periodicity means that if they wander apart, they're unlikely to
ever come back together.

John

Anthony Cruz wrote:

> Hi User:
> I have a little question. I planning to run a implicit solvent simulation of
> two peptides. The total system charge is 6. How I can setup the saltcon value
> to neutralize the total system charge????
>
> Best regards
> Anthony
>
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