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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:#4D54DB'>zoe.hall@chem.ox.ac.uk<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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