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.abra...@anu.edu.au
<mailto:mark.abra...@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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