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Hi Mikhail,<br>
<br>
we hard-coded the flat-bottom potential into bondfree.c which is in
src/gmxlib. I send you the source file in a separate e-mail.<br>
<br>
The patch will replace all position restraints by a flatt-bottom
spherical potential with a flat radius of 1.4nm. If you want a
different radius you'll have to change the bondfree.c, look for the
posre function. It's a quite dirty inflexible hack, but it was good
enough for us. So you cannot have normal position restraints and the
flat-bottom restraints at the same time.<br>
<br>
Note that you must define the reference position of all the position
restraint potentials with the -r option of grompp. E.g., if your
droplet is at the origin, you need a gro/pdb file with all
coordinates set to 0,0,0 to be used with the -r option. The position
restraints are defined as usual in the [ position_restraints ]
sections in the topology.<br>
<br>
I hope this helps, please let us know if something is unclear.<br>
<br>
Jochen<br>
<br>
On 10/17/11 Oct 17,2:41 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></p>
<p class="MsoNormal"><span style="font-weight:normal">Thank you
very much in advance.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-weight:normal">Mikhail<o:p></o:p></span></p>
<p class="MsoNormal"><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span
style="font-family:"Arial","sans-serif";font-weight:normal"
lang="EN-GB">=============================================<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-family:"Arial","sans-serif";font-weight:normal"
lang="EN-GB">Dr Mikhail Stukan<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-family:"Arial","sans-serif";font-weight:normal">Schlumberger
Dhahran Carbonate Research Center,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-family:"Arial","sans-serif";font-weight:normal">Dhahran
Techno Valley - KFUPM,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-family:"Arial","sans-serif";font-weight:normal">P.O.
Box 39011, Dammam / Doha Camp 31942,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-family:"Arial","sans-serif";font-weight:normal">Kingdom
of Saudi Arabia</span><span
style="font-family:"Arial","sans-serif";font-weight:normal"><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-family:"Arial","sans-serif";font-weight:normal"
lang="EN-GB">Tel: +966 3 331 6182<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-family:"Arial","sans-serif";font-weight:normal"
lang="EN-GB">Fax:+966 3 330 0845<br>
<a moz-do-not-send="true" href="mailto:mstukan@slb.com"><span
style="color:blue">mstukan@slb.com</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<pre class="moz-signature" cols="72">--
---------------------------------------------------
Dr. Jochen Hub
Computational and Systems Biology
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4715056 Fax: +46-18-511755
<a class="moz-txt-link-freetext" href="http://xray.bmc.uu.se/~jochen/index.html">http://xray.bmc.uu.se/~jochen/index.html</a>
---------------------------------------------------
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