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On 29/06/2011 7:08 PM, manana koberidze wrote:
<blockquote
cite="mid:BANLkTi=NZVdjhb++FYe+uE3QmDQyOW=tLw@mail.gmail.com"
type="cite">
<div class="gmail_quote">Thank you Mark, what puzzles me here is
summation, if it was only one term than it would be clear. <br>
</div>
</blockquote>
<br>
But a normal Coulomb interaction has the form E_i = q_i * SUM{q_j /
r_ij} summing over the other atoms j. If you can cast the
electrostatic component of the energy into a form dependent only on
the inter-atomic distance and atomic charge (as above) then using
the tabulated non-bonded interactions already implemented in GROMACS
is straightforward. See manual. If you need a different interaction
for each pair of atom types, then that is doable, but you'll have to
make a lot of energy groups and corresponding table files and accept
not-very-good performance - but I don't think you need this.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTi=NZVdjhb++FYe+uE3QmDQyOW=tLw@mail.gmail.com"
type="cite">
<div class="gmail_quote">Generally, if there is no other way than
changing the source code which files must be modified?Is there
any information about it anywhere? I found just the list of
files but for bonded interaction in the manual.
<div>
<br>
Thanks again<br>
<br>
</div>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
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On 28/06/2011 8:49 PM, manana koberidze wrote:<br>
> Dear All,<br>
><br>
> I've just started using GROMACS, I've read the manual and
searched the<br>
> mailing list but still confused. I'm trying to simulate
metal<br>
> oxidation with GROMACS. As a first step, I'm trying to
tabulate the<br>
> EAM (Embedded atom potential), which in addition to
residual pair-pair<br>
> repulsion includes the energy required to embed atom i in
a local<br>
> electron density rho, where rho is defined as:<br>
>
rho_i=SUM{k_j*exp(-beta_j*(r_ij-r*_j)) }<br>
> k, beta, r*_j are known parameters and the sum runs over
all other atoms.<br>
><br>
> Is there any way to tabulate the energy functional of
such local<br>
> electron density?<br>
<br>
Since it depends only on inter-atomic coordinates, it should
be<br>
possible. Before that, get some experience with normal GROMACS
simulations.<br>
<br>
Mark<br>
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<br>
-- <br>
<font size="2">Manana Koberidze<br>
<br>
</font><font size="2">Graduate Student<br>
Department of Applied Physics<br>
Aalto University School of Science <br>
P.O.Box 11100<br>
FI-00076 AALTO<br>
Finland<br>
Tel: +358-9-470 23137<br>
E-mail: manana.koberidze (at) <a moz-do-not-send="true"
href="http://aalto.fi" target="_blank">aalto.fi</a><br>
Office: Y229e main building (2nd floor)</font><br>
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