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<p class=MsoNormal>Dear GMXusers,<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I am trying to perform NVT on my solvated protein-lipid
system. After inserting the protein into the lipid using inflategro and a round
of energy minimization, I performed a 100ps NVT with position restraint only on
the protein molecule using (posre.itp).<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>After 100ps of NVT, the bilayer separated. As a result, I am
now trying to redo the NVT step, this time probably with position restraints on
the protein AND the P8 atom of my POPC (lipid_posre.itp). <o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I have in my .top file<o:p></o:p></p>
<p class=MsoNormal>;Protein<o:p></o:p></p>
<p class=MsoNormal>#include “protein.itp”<o:p></o:p></p>
<p class=MsoNormal>#ifdef POSRES<o:p></o:p></p>
<p class=MsoNormal>#include “posre.itp”<o:p></o:p></p>
<p class=MsoNormal>#endif<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>;Lipid<o:p></o:p></p>
<p class=MsoNormal>#include”popc.itp”<o:p></o:p></p>
<p class=MsoNormal>#ifdef POSRES_LIPID<o:p></o:p></p>
<p class=MsoNormal>#include “lipid_posre.itp”<o:p></o:p></p>
<p class=MsoNormal>#endif<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>When it comes to the .mdp file, I wonder how do I include
both <o:p></o:p></p>
<p class=MsoNormal>define = -DPOSRES and define = -DPOSRES_LIPID ? <o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Another quick question, is it advisable to do “trjconv
–pbc mol” on my system after every energy minimization/ MD to get an
unbroken structure before I carry on further?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Thanks a lot<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>HW<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
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