[gmx-users] Simulation of a charged system

[Surya Prakash Tiwari]

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


Thanks.

Regards,
Surya Prakash Tiwari



On Tue, Dec 6, 2011 at 23:15, Mark Abraham <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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