<div><font class="Apple-style-span" face="verdana, sans-serif"><span class="Apple-style-span" style="background-color: rgb(255, 255, 255); "><pre style="font-size: medium; color: rgb(0, 0, 0); font-family: 'Times New Roman'; ">
Liu, Liang wrote:
><i> > Thanks.
</i>><i> >
</i>><i> > Is this position restraint same to the one "Position Restrained
</i>><i> MD". I
</i>><i> > see some tutorial shows there are always three step to perform a
</i>><i> > simulation: Energy minimization, Position Restrained MD and MD
</i>><i> Simulation.
</i>><i>
</i>><i> "Always" is too strong, but this is common.
</i>><i>
</i>><i> > Is it possible to fulfill the position restraint during Position
</i>><i> > Restrained MD? Thanks.
</i>><i>
</i>><i> Yes, hence the name. How well they can be fulfilled depends on the
</i>><i> initial and simulation conditions.
</i>><i>
</i>><i>
</i>><i> Thanks for this information.
</i>><i> But how to perform a harmonic potential to all the heavy atoms of RNA?
</i>><i> Justin said this one should be adjusted in the posre.itp file, and what
</i>><i> I see in the file is all 1000. Does this means k=1000 in the equation of
</i>><i> E = k (r-r0)^2?
</i>
Yes. See my previous message. I explained the contents of the file, which are
also discussed in the manual.
-Justin</pre><pre style="font-size: medium; color: rgb(0, 0, 0); font-family: 'Times New Roman'; "><br></pre><pre style="font-size: medium; color: rgb(0, 0, 0); font-family: 'Times New Roman'; ">-----------------------------------------------------------------------------------</pre>
<pre><font class="Apple-style-span" face="verdana, sans-serif" color="#3333ff">perfect, thanks a lot.</font></pre><pre><font class="Apple-style-span" face="verdana, sans-serif" color="#3333ff">Does this conflict with the bond restraint, e.g. LINCS algorithm, during simulation?</font></pre>
</span></font></div>-- <br>Best,<br>Liang Liu<br>