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On 17/10/2011 11:41 PM, Mikhail Stukan wrote:
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<p class="MsoNormal"><span style="font-weight:normal">Dear
gmx-user,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">I would
like to simulate an isolated drop of water (without PBC).
To prevent water molecules form evaporation I would like to
create a spherical constraint around the system. In recent
article in PNAS (Caleman, Hub, van Maaren, van der Spoel,
v. 108, 6838 (2011)) where the authors considered similar
system it is mentioned that:<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span
style="font-size:10.0pt;font-family:"AdvOT10f0fcb1","sans-serif";font-weight:normal">“To
avoid such evaporation, we applied a spherical flat-bottom
quadratic potential acting on the water. That potential was
implemented as an additional force </span><span
style="font-size:10.0pt;font-family:"AdvOT92137dae.I","sans-serif";font-weight:normal">F
</span><span
style="font-size:10.0pt;font-family:"AdvOT10f0fcb1","sans-serif";font-weight:normal">pointing
toward the COM of the droplet…”<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">Could
anybody give a hint how this approach can be realized in
GROMACS? I looked through the manual, but did not find
clear answer how to implement such a force.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal"><o:p> </o:p></span><br>
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<br>
I think the only way to do something like this in GROMACS is with a
COM virtual site and such a distance restraint from each water
molecule to that virtual site.<br>
<br>
Mark<br>
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