Thanks Mark for the reply. I didn't find anything in AMBER manual. I emailed the author of that paper.<br><br>I have one more question:<br><br>Whether <i>charged system correction term</i> (-(1/(8*epsilon_0*kappa^2*L^3))*(Sum over q^2)) has been implemented in the PME implementation of Gromacs. <br>
<br>I am talking about the last term of eqn. 15 on page 8 of the following paper:<br><br>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<br>
<br><br>Thanks.<br><br>Regards,<br>Surya Prakash Tiwari<br><br><br><br>On Tue, Dec 6, 2011 at 23:15, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:<br>> On 7/12/2011 11:31 AM, Surya Prakash Tiwari wrote:<br>
>><br>>> Dear Gromacs users,<br>>><br>>> I am simulating a charged system with periodic boundary conditions. My<br>>> system has 506 water molecules and one ion.<br>>> I am trying to calculate the free energy of an ion.<br>
>> I do not want to use any counter-ions to neutralize the system,<br>>> because I don't have force-field between my ion and the counterion.<br>>><br>>> In particular, I want to reproduce the following paper: <br>
>> Horinek, D., Mamatkulov, S. I.,& Netz, R. R. (2009). Rational design<br>>><br>>> of ion force fields based on thermodynamic solvation properties. The<br>>> Journal of chemical physics, 130(12), 124507. doi:10.1063/1.3081142<br>
>><br>>> Their system is also charged, has one ion and 506 water molecules.<br>>> They are using AMBER software. On page number 7, they have discussed<br>>> the correction terms due to ewald summation (equation 6) in a charaged<br>
>> system.<br>>> On the same page, they further say that AMBER has implemented first<br>>> term in eqn. 6 to account for ion’s Coulomb interaction with its<br>>> periodic images:<br>>> "In the PME implementation in AMBER, a self-energy correction of<br>
>> N*e^2 *xi /(8*pi*epsilon) is already accounted for."<br>>><br>>> I just want to know whether, Gromacs has the same implementation in<br>>> their PME to account for ion’s Coulomb interaction with its periodic<br>
>> images.<br>><br>><br>> Sounds strange to me. I'd check the AMBER manual for what this is and how it<br>> works (don't think you'll find anything) and then ask the authors of that<br>> paper what they really mean. As Darden et al note (JCP 109 10921) at the end<br>
> of section IIB, the so-called "self term" and the "self potential" are<br>> different things, and this is possibly a problem.<br>><br>> Mark<br>> --<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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