AMBER Archive (2009)

Subject: Re: [AMBER] general query: implicit solvation

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Sep 08 2009 - 05:11:24 CDT

The goal of these models is to properly solvate the atoms according to
their solvent exposure, but atoms below the surface are affected by
solvent so it isn't as simple as you suggest, even with explicit water.

On Sep 8, 2009, at 5:28 AM, Jio M <jiomm_at_yahoo.com> wrote:

> Dear Amber users
>
>
>
> I have general query (may be silly)
>
> we do simulations in implicit solvents especially for protiens or
> macromolecules which have many atoms inside and outside the dense
> structure..but if we compare it with explicit solvent only external
> atoms get interacted with solvent atoms (if solvent is not
> accesible to inside atoms of the dense core)
>
>
>
> my query is when we consider implicit solvation all the atoms will be
> considered in implicit solvent (whether they are inside or outside)..
> so is it not that we are "Over-expressing" the interactions because as
> a rule only outside atoms should be considered
>
>
>
> or else the interactions are already designed in implicit that only
> outside atoms are considered.....
>
>
>
> thanks and regards
>
>
>
> Jiomm
>
>
>
>
>
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