On Thu, May 17, 2018, PRITI ROY wrote:
>
> I want to calculate the solvation free energy of my system through 3D-RISM
> and this is my first time approach of this method. Before going to this
> step I need to get bulk water information which done by 1D-RISM. I have
> used TIP3P water model with Na+ ions. My input file is as follows:
As pointed out in a separate email, the size of the grid needed for a
bulk (rism1d) simulation is not related to the eventual size of your
3drism box.
You can see sample rism1d inputs in $AMBERHOME/AmberTools/test/rism1d:
try to build off of those.
Your input file has some very odd choices: first you have water and
sodium ions, but no anions. While this is not technically impossible,
it doesn't make physical sense, and is almost certainly will cause all
kinds of problems, especially for someone new to these calcualations.
Your solvent needs to be electrically neutral.
> TEMPER=310, DIEps=95.0,
This is a very high dielectric constant: are you sure this is what you
want?
> &SPECIES
> units='g/cm^3'
> DENSITY=2.85,
> MODEL="../TP3.mdl"
Also a very odd density. Again, are you sure this is what you want?
I don't think one would expect our simple models of water to work at all
well under such conditions, even if you could get the RISM equations to
converge.
....dac
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Received on Thu May 17 2018 - 09:30:02 PDT
