AMBER Archive (2006)

Subject: Re: AMBER: Implicit solvent question

From: Anthony Cruz (acb15885_at_uprm.edu)
Date: Thu Jun 29 2006 - 11:44:54 CDT

Thank you for your answer.
How I can keep then together? because as soon as the simulation start the
peptides start to unfold and to separate from each other.

Setting the distance between the petides > cutoff and rgbmas = cutoff could
resolve the problem???

Best regards
 Anthony

On Friday 23 June 2006 12:09 pm, John Mongan wrote:
> 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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