Re: Protein solvation

From: Kipp Johnson (
Date: Sat May 10 2014 - 15:38:26 CDT

Do you mean blood plasma?

Blood plasma is mostly water with relatively high concentrations of Na+ and
Cl-, and some K+, Ca2+, and bicarbonate: I imagine you could add those to a
system with VMD's autoionize plugin.

Adding and simulating the additional glucose, hormones, clotting factors,
variety of proteins (!), CO2, etc. present in plasma would be a different

On Sat, May 10, 2014 at 12:28 PM, farzad kiani <> wrote:

> Hi,
> Dear NAMD users
> I want to simulate a protein with it target in Plasma to calculate the
> adsorption energy
> I want to simulate real physics of the problem
> I think in real physic of the problem the salt concentration is too much
> low
> Dose any one now how should I solvate the protein and its target in
> plasma: in not ionized water or in ionized water?
> Does it true if solvate them in not ionized water?
> Best regards
> Farzad Kiani

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