<p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;"><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;">Hi Justin,</p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><blockquote style="font-family: Gulim; font-size: 12px; border-left-style: solid; border-left-width: 2px; margin: 0pt 0pt 0pt 0.8em; padding-left: 1em;"><div style="font-family:arial,돋움;line-height:1.5"><div style="margin-top:5px;"><pre>
> Meanwhile, is it possible to implement a self-consistent FF from scratch? One
> example I came across is from the work by Ho and Striolo
>
> titled: Polarizability effects in molecular dynamics simulations of the
> graphene-water interface
>
Of course you can implement whatever you like. Gromacs has been able to carry
out polarizable simulations for a very long time; I've only ever cautioned
against abuse of certain models.
</pre></div></div></blockquote><font face="monospace"><br>I guess that GROMACS is capable in running polarisable sims, but for the Drude polarisable calcs, they are prone to polarisation catastrophe due to the massless shells and thermostat instability?<br>In the paper mentioned above, the authors have carried out three types of cals:<br>i) SPC/E on non-pol graphene <br>ii) SWM4-DP on non-pol graphene: graphene in neutral or charged states<br>iii) SWM4-DP on graphene-DP (one Drude particle per C-atom with opposite charge): graphene-DP in neutral or charged states<br><br></font><span style="font-family: monospace;">They seemed to have simulated their systems using both additive and polarisable (0.878 angstrom^3) models?</span><font face="monospace"><br></font><span style="font-family: monospace;">I guess this is where I got confused. </span><font face="monospace"><br></font><font face="monospace"><br>On the side: From my previous calcs using GRAPPA force field (TIPS3P water model), graphene's polarisation (0.91 </font><span style="font-family: monospace;">angstrom^3</span><font face="monospace">) resulted in spreading of water into thin layer. But that was polarisable graphene in a rigid rod model (dummy instead of shelltype particle). <br><br><br><span style="font-size: 12px; line-height: 18px; white-space: pre;"><br></span></font><blockquote style="font-family: Gulim; font-size: 12px; border-left-style: solid; border-left-width: 2px; margin: 0pt 0pt 0pt 0.8em; padding-left: 1em;"><div style="font-family:arial,돋움;line-height:1.5"><div style="margin-top:5px;"><pre>
>
> Pardon me if this sounds outright wrong; regarding the massless Drude particle,
> can it be replaced with an atom (assuming an induced dipole model) instead of
> the charge-on-spring model? The mass of the atom can be set to 0.4 amu with an
> opposite charge of the water oxygen atom?
>
In the Drude model with 0.4-amu particles, the Drudes are essentially just
atoms. There's nothing conceptually special about them, we just handle them
slightly differently in the code.
</pre><pre><br></pre></div></div></blockquote><font face="monospace">Well since domain decomposition will not work on shelltype calcs, I am intrigued to experiment if I can:<br>i) replace the Drudes to atom with the same configuration - opposite charge, mass (0.4 amu), lengths, etc<br><br>OR <br><br>ii) switch to the more stable SWM4-DP with the hydronium and hydroxide implementation from David van der Spoel?<br><br>Regards,<br>Kester<br><br><br><br><br><span style="font-size: 12px; line-height: 18px; white-space: pre;"><br></span></font><blockquote style="font-family: Gulim; font-size: 12px; border-left-style: solid; border-left-width: 2px; margin: 0pt 0pt 0pt 0.8em; padding-left: 1em;"><div style="font-family:arial,돋움;line-height:1.5"><div style="margin-top:5px;"><pre><br></pre></div></div></blockquote></p>
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