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On 12/01/2011 2:29 AM, Zoe Hall wrote:
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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>
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<br>
vdwtype = cut-off<br>
coulombtype = cut-off<br>
<br>
and all the distance cut-offs to zero (which is treated as an
infinite cut-off)<br>
<br>
Mark<br>
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