<p class="MsoNormal"><a name="12fe9d9619177279_OLE_LINK1"><span lang="EN-US">Dear Justin</span></a></p>
<p class="MsoNormal"><span><span lang="EN-US"> </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">Thanks
for your reply. Generally I conduct the simulation following the tutorial on your
website. The system contains an integrin alpha2b/beta3 transmembrane portion
(PDB 2KNC) embedding in a 124-lipids DPPC bilayer and solvated in water. The initial
membrane-protein system is built with INFLATEGRO. Here is the topology file of
the system (not completed):</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">“</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">;
Include forcefield parameters</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">#include
"ffG53a6_lipid.itp"</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"> </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">;
Include chain topologies</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">#include
"topol_A.itp"</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"> </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">;
Include Position restraint file</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">#ifdef
POSRES</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">#include
"posre_A.itp"</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">#endif</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"> </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">#include
"topol_B.itp"</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"> </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">;
Include Position restraint file</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">#ifdef
POSRES</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">#include
"posre_B.itp"</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">#endif</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"> </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">;
Include DPPC chain topology</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">#include
"dppc.itp"</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"> </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">;
Include water topology</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">#include
"spc.itp"</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"> </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">#ifdef
POSRES_WATER</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">;
Position restraint for each water oxygen</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">[
position_restraints ]</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">;<span> </span>i funct<span>
</span><span> </span>fcx<span> </span>fcy<span> </span>fcz</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"><span> </span>1<span>
</span>1<span> </span>1000<span> </span>1000<span> </span>1000</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">#endif</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"> </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">;
Include generic topology for ions</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">#include
"ions.itp"</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"> </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">[
system ]</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">; Name</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">Protein
in water</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"> </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">[
molecules ]</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">;
Compound<span> </span>#mols</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">Protein_A<span> </span>1</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">Protein_B<span> </span>1</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">DPPC
124</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">SOL<span> </span>17185</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">NA+ 2</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">”</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"> </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">For
the details of energy minimization, here is one of the mdp files for energy
minimization:</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">“</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">define
= -DPOSRES</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">integrator
= cg</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">emtol
= 500.0<span> </span><span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">emstep
= 0.01<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">nstcgsteep
= 100</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">nsteps<span> </span>= 50000<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"> </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">nstlist
= 1<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">ns_type
= grid<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">rlist
= 1.2<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">coulombtype
= PME<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">rcoulomb
= 1.2<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">rvdw =
1.2<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">pbc =
xyz </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"> </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"> </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">freezegrps
= Protein-H</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">freezedim
= Y Y Y<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">”</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">As you
may notice, I froze the heavy atoms of the protein during the first energy minimization
and then in the following the EMs the frozen
group was MainChain, C-alpha and none in order. The system finally reached Fmax < 500. </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"> </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">The
similar method was employed in the NPT equilibration and here is one of the mdp
files:</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">“</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">title
= NPT Equilibration<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">define<span> </span>= -DPOSRES</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">integrator
= md<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">nsteps<span> </span>= 100000 </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">dt =
0.0005<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">nstxout
= 100<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">nstvout
= 100<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">nstenergy
= 100<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">nstlog<span> </span>= 100</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"><span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">continuation<span> </span>= yes<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">constraint_algorithm
= lincs </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">constraints
= none<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">lincs_iter
= 1 </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">lincs_order
= 4<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"> </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">ns_type
= grid<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">nstlist
= 5<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">rlist
= 1.2<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">rcoulomb
= 1.2<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">rvdw =
1.2<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">coulombtype
= PME<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">pme_order
= 4<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">fourierspacing
= 0.16<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"> </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">tcoupl<span> </span>= Nose-Hoover<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">tc-grps
= Protein DPPC SOL_NA+<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">tau_t =
0.5<span> </span>0.5<span> </span>0.5<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">ref_t =
323 <span> </span>323<span> </span>323</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"> </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">pcoupl
= Parrinello-Rahman<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">pcoupltype
= semiisotropic<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">tau_p =
2.0<span> </span>2.0</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">ref_p =
1.0<span> </span>1.0<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">compressibility
= 4.5e-5<span> </span>4.5e-5<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"> </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">pbc =
xyz<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"> </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">DispCorr
= EnerPres<span> </span></span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"> </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">gen_vel
= no</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">gen_temp
= 323</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">gen_seed
= -1</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"> </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">nstcomm
= 1</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">comm-mode
= Linear</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">comm-grps
= Protein_DPPC SOL_NA+</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"> </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">freezegrps
= Protein-H</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">freezedim
= Y Y Y </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">”</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"> </span></span></p>
<p class="MsoNormal"><span><span lang="EN-US">Hope
those information may help you and others understand my problem.</span></span></p>
<p class="MsoNormal"><span><span lang="EN-US"><br></span></span></p>
Li<br>