[gmx-users] Simulation of a charged system

[Mark Abraham]

On 8/12/2011 3:21 PM, Surya Prakash Tiwari wrote:
> Thanks Mark for the reply. I didn't find anything in AMBER manual. I 
> emailed the author of that paper.
>
> I have one more question:
>
> Whether /charged system correction term/ 
> (-(1/(8*epsilon_0*kappa^2*L^3))*(Sum over q^2)) has been implemented 
> in the PME implementation of Gromacs.
>
> I am talking about the last term of eqn. 15 on page 8 of the following 
> paper:
>
> ?Warren, G. L., & Patel, S. (2007). Hydration free energies of 
> monovalent ions in transferable intermolecular potential four point 
> fluctuating charge water: an assessment of simulation methodology and 
> force field performance and transferability. The Journal of chemical 
> physics, 127(6), 064509. doi:10.1063/1.2771550

Yes. See ewald_LRcorrection() in src/gmxlib/ewald_util.c

Mark

>
>
> Thanks.
>
> Regards,
> Surya Prakash Tiwari
>
>
>
> On Tue, Dec 6, 2011 at 23:15, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
> > On 7/12/2011 11:31 AM, Surya Prakash Tiwari wrote:
> >>
> >> Dear Gromacs users,
> >>
> >> I am simulating a charged system with periodic boundary conditions. My
> >> system has 506 water molecules and one ion.
> >> I am trying to calculate the free energy of an ion.
> >> I do not want to use any counter-ions to neutralize the system,
> >> because I don't have force-field between my ion and the counterion.
> >>
> >> In particular, I want to reproduce the following paper: ?
> >> Horinek, D., Mamatkulov, S. I.,&  Netz, R. R. (2009). Rational design
> >>
> >> of ion force fields based on thermodynamic solvation properties. The
> >> Journal of chemical physics, 130(12), 124507. doi:10.1063/1.3081142
> >>
> >> Their system is also charged, has one ion and 506 water molecules.
> >> They are using AMBER software. On page number 7, they have discussed
> >> the correction terms due to ewald summation (equation 6) in a charaged
> >> system.
> >> On the same page, they further say that AMBER has implemented first
> >> term in eqn. 6 to account for ion's Coulomb interaction with its
> >> periodic images:
> >> "In the PME implementation in AMBER, a self-energy correction of
> >> N*e^2 *xi /(8*pi*epsilon) is already accounted for."
> >>
> >> I just want to know whether, Gromacs has the same implementation in
> >> their PME to account for ion's Coulomb interaction with its periodic
> >> images.
> >
> >
> > Sounds strange to me. I'd check the AMBER manual for what this is 
> and how it
> > works (don't think you'll find anything) and then ask the authors of 
> that
> > paper what they really mean. As Darden et al note (JCP 109 10921) at 
> the end
> > of section IIB, the so-called "self term" and the "self potential" are
> > different things, and this is possibly a problem.
> >
> > Mark
> > --
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