Dear David,
Thank you for such an effort and giving your valuable comment.
I have searched in the literature about Di-electric constant of TIP3P water
model and I got to know this model has higher value than other simple
3-point models. Here is one of the reference:
https://aip.scitation.org/doi/pdf/10.1063/1.477104 (The reason for using
such an high value)
In my protein water complex system I have only Na+ ions, that's why I took
only this ion.
I figure out that main failure of my calculation is the density. I
rechecked the density which is around 0.96 gm/cm^3. Now I can run the
1D-Rism using the Na+ and water using the mentioned density.
Best,
Priti
On Thu, May 17, 2018 at 9:41 PM, David A Case <david.case.rutgers.edu>
wrote:
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 17 2018 - 22:30:03 PDT
