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Zoe Hall skrev 2011-01-11 16.29:
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi gmx-users,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am trying to set up a simulation of a
large protein <i>in
vacuo</i> using the OPLS-AA forcefield, with conditions
based on Patriksson et.
al (Biochemistry 2007, 46 p933). Basically after energy
minimisation, the
protein is run for 10ps in vacuum with constant temperature at
300K. This is
followed by the full production run of 10ns with temperature
and pressure
coupling turned off, H bonds are constrained using SHAKE with
tolerance 0.001.
For vacuum conditions, the periodic boundary conditions are
turned off, and no
cut-offs are used whatsoever. <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am not sure, however, what is the
appropriate choice for
“coulombtype” and other electrostatic parameters for vacuum
simulations. I have
set “epsilon_r” to 2, as this seems to be an accepted value
for proteins but if
anyone has comments on this, I would appreciate it.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks very much,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Zoe <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Zoe Hall <o:p></o:p></p>
<p class="MsoNormal">Department of Chemistry<o:p></o:p></p>
<p class="MsoNormal">Oxford University<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><u><span style="color: rgb(77, 84, 219);"><a class="moz-txt-link-abbreviated" href="mailto:zoe.hall@chem.ox.ac.uk">zoe.hall@chem.ox.ac.uk</a><o:p></o:p></span></u></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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I should point out that there is probably an error in the methods
section. If I recall correctly we used a 0.5 fs timestep. We
couldn't get good conservation of total energy with 1 fs steps.
Remember to use double precision, or you will again loose
conservation of total erergy. Remember to monitor the total energy,
because if it's drifting you need to have a more conservative setup,
e.g., use a smaller timestep.<br>
<br>
Take a look at our "follow up" study (Marklund et. al., PCCP (2009)
11 p. 8069–8078) where we used LINCS and managed to conserve the
total energy with a 1 fs time step.<br>
<br>
Good luck!<br>
<br>
<pre class="moz-signature" cols="72">--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
<a class="moz-txt-link-abbreviated" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a class="moz-txt-link-freetext" href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se/</a>
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