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On 28/06/2011 8:49 PM, manana koberidze wrote:
<blockquote
cite="mid:BANLkTinriVPiCmDpHpEE6U1us+YyjDGy2w@mail.gmail.com"
type="cite">Dear All,<br>
<br>
I've just started using GROMACS, I've read the manual and searched
the mailing list but still confused. I'm trying to simulate metal
oxidation with GROMACS. As a first step, I'm trying to tabulate
the EAM (Embedded atom potential), which in addition to residual
pair-pair repulsion includes the energy required to embed atom i
in a local electron density rho, where rho is defined as:<br>
rho_<font size="2">i</font>=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
electron density?<br>
</blockquote>
<br>
Since it depends only on inter-atomic coordinates, it should be
possible. Before that, get some experience with normal GROMACS
simulations.<br>
<br>
Mark<br>
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