[gmx-users] Solvent density around a Protein

Hans Wurst Maikleuschner at hotmail.com
Mon Oct 12 14:40:13 CEST 2015


I want to examine a Myoglobine-ethylene glycole-water system and I am trying to calculate the density of ethylene glycole and the density of water around residues of Myoglobin (for example Valine).

In the mailinglist I found the advice to use the gromacs tool g_sorient to get a distribution of the solvent molecules as a function of the radius around a reference point.

One can find in the manual that the solvent molecules should consist of 3 atoms. So I can easily do this for water (3 atoms). I tried using g_sorient for ethylene glycole (6 atoms) too but the ethylene glycole distribution seems to be twice as high as they should be.

Now I am asking myself whether the real ethylene glycole distribution is exactly the half of the values that gromacs calculates?

In case I get completely wrong values for the distribution, is there another tool to calculate the ethylene glycole distribution around protein residues?

Thanks in advance,


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