Dear Meisam,<br>Take a look at Justin Lemkul's tutorial. It's very well explained step by step: <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html</a><br>
Good luck,<br>Marcelo<br><br><div class="gmail_quote">On Tue, Sep 27, 2011 at 10:49 AM, meisam valizadeh kiamahalleh <span dir="ltr"><<a href="mailto:meisam488@gmail.com">meisam488@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<p class="MsoNormal"><span lang="EN-US">Dear GMX Users</span></p><p class="MsoNormal"><span lang="EN-US">I would
like to let you know that I have run MD simulation on a Carbon nanotube- drug
system.</span></p>
<p class="MsoNormal"><span lang="EN-US">All steps (Energy
minimization, Postion restrained, Equilibration with NVT and NPT ensembles and
finally MD) have been done successfully. Currently if would like to calculate binding
free energy for the system (drug molecules inside Carbon nanotube). Here are my
questions at this point;</span></p><p class="MsoNormal"><span lang="EN-US">1.</span>May I know if I must add the free
energy stuff to all the mdp files for each steps of (Energy minimization, Position
restrained, Equilibration with NVT and NPT ensembles and finally MD) and redo all
the simulation steps? I am wondering because I have seen few people who only edited
the final MD.mdp file and add the free energy stuff.</p><p class="MsoNormal"><br></p><p class="MsoNormal"><span lang="EN-US"><span><span style="font:7.0pt "Times New Roman""><font face="arial" size="2">2.</font> </span></span></span><span lang="EN-US">I know to get the binding energy curve;
I need to </span>run several simulations, one for each lambda value. <span> <span lang="EN-US">Hence, I need 21 point from Lambda=0
to 1 to get the smooth curve. To do this, I have to start with initial Lambda
=0 as stated in the energy stuff below, in my mdp file.<span> </span>May I know which parameter(s) (init_lambda or foreign lambda or ...) need to be changed
in my mdp file to do the next simulation and until the last simulation? I mean
to go from Lambda=0.0 to the next lambda =0.05, 0.10, 0.15, … and 1.00.</span></span></p>
<p class="MsoNormal"><span lang="EN-US">The free
energy stuff in my mdp file is as below:</span></p><p class="MsoNormal"><br></p><p class="MsoNormal">; Free
energy control stuff</p><p class="MsoNormal">free_energy<span> </span>= yes</p><p class="MsoNormal">init_lambda<span> </span>= 0.00</p><p class="MsoNormal">delta_lambda<span> </span>= 0</p>
<p class="MsoNormal">foreign_lambda<span> </span>= 0.05</p><p class="MsoNormal">sc-alpha<span> </span>= 0.5</p><p class="MsoNormal">sc-power<span> </span>= 1.0</p><p class="MsoNormal">
sc-sigma<span> </span><span> </span>= 0.3</p><p class="MsoNormal"><br></p><p class="MsoNormal">Your kind advice on this matter would be highly appreciated.</p><p class="MsoNormal">Best regards</p><p class="MsoNormal">
Meisam</p>
<br>--<br>
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Marcelo F. Masman, Ph.D.<br>Department of Molecular Neurobiology,<br>Faculty of Mathematics and Natural Sciences,<br>University of Groningen.<br><span style="color:rgb(0, 0, 0)">
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