<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;"></p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"></p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"></p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;">Hi Justin and all, </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.
>
>
> 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?
Polarization catastrophe is possible in any polarizable simulation. Usually
very small time steps are required to avoid this, unless using an anharmonic
potential or a hard wall restraint.
</pre><pre><br></pre></div></div></blockquote><font face="monospace" style="font-family: Gulim; font-size: 10pt;">Using Morse = yes for the anharmonic potential option, whereas using the parameters below for the hard wall restraint option?<br><br>pbc = xy<br>nwall = 2<br>wall-atomtype = ; optional<br>wall-type = 12-6<br>wall-r-linpot = 1 ; having a positive val. is esp. useful in equil. run<br>wall-density = 5 5<br>wall-ewald-zfac = 3<br><br><br></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>> In the paper mentioned above, the authors have carried out three types of cals:
> i) SPC/E on non-pol graphene
> ii) SWM4-DP on non-pol graphene: graphene in neutral or charged states
> iii) SWM4-DP on graphene-DP (one Drude particle per C-atom with opposite
> charge): graphene-DP in neutral or charged states
>
> They seemed to have simulated their systems using both additive and polarisable
> (0.878 angstrom^3) models?
> I guess this is where I got confused.
I suppose you can make any model work if you parametrize it a certain way, but
my point in the previous message is that you shouldn't go off trying to build a
force field that has SWM4-NDP water around additive CHARMM solutes.
</pre></div></div></blockquote><font face="monospace" style="font-family: Gulim; font-size: 10pt;"><br>Yep, now I understand it. <br></font>If I wanted to also describe graphene, is it possible to include carbon parameters in the SWM4-NDP force field then?<font face="monospace" style="font-family: Gulim; font-size: 10pt;"><br><br><br></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>>
> On the side: From my previous calcs using GRAPPA force field (TIPS3P water
> model), graphene's polarisation (0.91 angstrom^3) resulted in spreading of water
> into thin layer. But that was polarisable graphene in a rigid rod model (dummy
> instead of shelltype particle).
>
>
>
> >
> > 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.
>
>
> Well since domain decomposition will not work on shelltype calcs, I am intrigued
> to experiment if I can:
> i) replace the Drudes to atom with the same configuration - opposite charge,
> mass (0.4 amu), lengths, etc
>
The problem is that shells/Drudes have to be relaxed (SCF) or otherwise have
their positions integrated (extended Lagrangian) separately from "normal" atoms.
Conceptually, a 0.4-amu Drude is just an atom, but the integration is carried
out differently, so no, this sort of hacked approach probably isn't very robust.
</pre></div></div></blockquote><font face="monospace" style="font-family: Gulim; font-size: 10pt;">You mean the relaxation during NVT, e.g. emtol = 0.1 and niter = 30?<br>As far as I know, for pure energy minimisation, the shells are treated just like any other particles, so what matters is the shell minimiser/integration differs than an "atom" during MD right?</font><div><br><p style="font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;">To relax a system containing Drude particles, is md=steep enough, or the more accurate conjugate gradient?</p><div>I get unreasonable energy minimised confout.gro structure very often, if there are Drude-based ions included (head-scratching).</div><div><span style="font-size: 10pt;"><br></span></div><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>> OR
>
> ii) switch to the more stable SWM4-DP with the hydronium and hydroxide
> implementation from David van der Spoel?
I don't know how this relates to the point above about graphene, so I'm a bit
lost. SWM4-NDP is a better model than SWM4-DP, FWIW.
</pre></div></div></blockquote><font face="monospace"><br>Absolutely, no doubt about that; SWM4-NDP describes water surf.tension better than SWM4-DP.<br>It was just a thought, that if SWM4-NDP becomes very unstable upon the inclusion of polarisable ions (e.g. hydronium and hydroxide that also contain Drude particle), SWM4-DP could be an alternative? <br></font><p style="font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><blockquote style="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.
>
>
> 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?
Polarization catastrophe is possible in any polarizable simulation. Usually
very small time steps are required to avoid this, unless using an anharmonic
potential or a hard wall restraint.
</pre><pre><br></pre></div></div></blockquote><font style="font-size: 10pt;">Using Morse = yes for the anharmonic potential option, whereas using the parameters below for hard wall restraint?<br><br>pbc = xy<br>nwall = 2<br>wall-atomtype = ; optional<br>wall-type = 12-6<br>wall-r-linpot = 1 ; having a positive val. is esp. useful in equil. run<br>wall-density = 5 5<br>wall-ewald-zfac = 3<br><br><br></font><blockquote style="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>> In the paper mentioned above, the authors have carried out three types of cals:
> i) SPC/E on non-pol graphene
> ii) SWM4-DP on non-pol graphene: graphene in neutral or charged states
> iii) SWM4-DP on graphene-DP (one Drude particle per C-atom with opposite
> charge): graphene-DP in neutral or charged states
>
> They seemed to have simulated their systems using both additive and polarisable
> (0.878 angstrom^3) models?
> I guess this is where I got confused.
I suppose you can make any model work if you parametrize it a certain way, but
my point in the previous message is that you shouldn't go off trying to build a
force field that has SWM4-NDP water around additive CHARMM solutes.
</pre></div></div></blockquote><font style="font-size: 10pt;"><br>Yep, now I understand it. <br></font>Is it possible to include the carbon parameters in the SWM4-NDP force field to describe/represent graphene?<font style="font-size: 10pt;"><br><br><br></font><blockquote style="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>>
> On the side: From my previous calcs using GRAPPA force field (TIPS3P water
> model), graphene's polarisation (0.91 angstrom^3) resulted in spreading of water
> into thin layer. But that was polarisable graphene in a rigid rod model (dummy
> instead of shelltype particle).
>
> >
> > 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.
>
>
> Well since domain decomposition will not work on shelltype calcs, I am intrigued
> to experiment if I can:
> i) replace the Drudes to atom with the same configuration - opposite charge,
> mass (0.4 amu), lengths, etc
>
The problem is that shells/Drudes have to be relaxed (SCF) or otherwise have
their positions integrated (extended Lagrangian) separately from "normal" atoms.
Conceptually, a 0.4-amu Drude is just an atom, but the integration is carried
out differently, so no, this sort of hacked approach probably isn't very robust.
</pre></div></div></blockquote><font style="font-size: 10pt;">You mean the relaxation during NVT, e.g. emtol = 0.1 and niter = 30?<br>As far as I know, for pure energy minimisation, the shells are treated just like any other particles, so what matters is the shell minimiser/integration differs than an "atom" during MD right?<br><br></font><blockquote style="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>> OR
>
> ii) switch to the more stable SWM4-DP with the hydronium and hydroxide
> implementation from David van der Spoel?
I don't know how this relates to the point above about graphene, so I'm a bit
lost. SWM4-NDP is a better model than SWM4-DP, FWIW.
</pre></div></div></blockquote><font face="monospace"><br>Absolutely, no doubt about that; SWM4-NDP describes water surf.tension better than SWM4-DP.<br>It was just a thought, that if SWM4-NDP becomes very unstable upon the inclusion of polarisable ions (e.g. hydronium and hydroxide that also contain Drude particle), SWM4-DP could be an alternative? <br><br><br>Thanks again for the information, really appreciate it.<br><span style="font-size: 12px; line-height: 18px; white-space: pre;"><br></span></font><blockquote style="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;"></div></div></blockquote><font face="monospace"><br>Regards,<br>Kester<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 style="font-family: Gulim; font-size: 10pt;"></p><p style="font-family: Gulim; font-size: 10pt;"></p><p style="font-family: Gulim; font-size: 10pt;"></p></div></p>
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