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On 8/12/2011 3:21 PM, Surya Prakash Tiwari wrote:
<blockquote
cite="mid:CAAC7PFLgDJ4hW2_Db_Fu+nX+WktVxzTsuhcBnV+jhxdE6-f2+A@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
Yes. See ewald_LRcorrection() in src/gmxlib/ewald_util.c<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAAC7PFLgDJ4hW2_Db_Fu+nX+WktVxzTsuhcBnV+jhxdE6-f2+A@mail.gmail.com"
type="cite">
<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
moz-do-not-send="true" 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>
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