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<p>Hey Pierre,</p>
<p><br></p>
<p>What exactly are you using to generate your structures? Strip the CONECT statements, they will be ignored, and it is not anything to worry about.</p>
<p>
<br>Alex</p>
<p><br></p>
<p><br></p>
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<p><span class=rvts7>Hello Alex, </span></p>
<p><br></p>
<p><span class=rvts7>Thank you a lot for your answer and I will do this tutorial again and again. </span></p>
<p><span class=rvts7>I have tried some generators for carbon nanotubes, and I always have : </span></p>
<p><br></p>
<p><span class=rvts8>WARNING: all CONECT records are ignored</span></p>
<p><span class=rvts8>Read X atoms</span></p>
<p><span class=rvts8>No velocities found</span></p>
<p><br></p>
<p><span class=rvts9>As you said, I have to check the PDB file. I try to check it by analogy with other simple PDB files but I do not know what is wrong in mine. I have Atom coordinates, connections lines are here. </span></p>
<p><br></p>
<p><span class=rvts9>Nevermind, I will work more on it! </span></p>
<p><br></p>
<p><span class=rvts9>Thank you a lot, </span></p>
<p><span class=rvts9>have a nice day / night. </span></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><span class=rvts10>Pierre BERTIN</span></p>
<p><span class=rvts11>Bioinformatics and Biostatistics student (MSc),</span></p>
<p><span class=rvts11>University Paris-Sud XI, ORSAY.</span></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><span class=rvts12>2015-04-11 13:41 GMT-06:00 Alex <</span><a class=rvts13 href="mailto:nedomacho@gmail.com">nedomacho@gmail.com</a><span class=rvts12>>:</span></p>
<p><br></p>
<p><span class=rvts12>Hi Pierre,</span></p>
<p><br></p>
<p><span class=rvts12>A standard CNT/graphene parameterization in GMX doesn't currently</span></p>
<p><span class=rvts12>exist, but if you're just playing around, please follow the Andrea</span></p>
<p><span class=rvts12>Minoia's tutorial (</span><a class=rvts13 href="http://www.webcitation.org/66u2xJJ3O">http://www.webcitation.org/66u2xJJ3O</a><span class=rvts12>) exactly. It</span></p>
<p><span class=rvts12>works, and there should be no errors. Make sure your initial PDB is</span></p>
<p><span class=rvts12>properly formatted. Also, you do not have to create GRO structures.</span></p>
<p><span class=rvts12>When you box your initial coordinates, you can set the output to .pdb,</span></p>
<p><span class=rvts12>which x2top and (later on) grompp will accept.</span></p>
<p><br></p>
<p><span class=rvts12>There are two issues with that tutorial:</span></p>
<p><span class=rvts12>1. The bond, angle, and dihedral constants are wrong, copied from</span></p>
<p><span class=rvts12>aromatics.</span></p>
<p><span class=rvts12>I am using constants derived from the optimized Brenner potential. For bond type</span></p>
<p><span class=rvts12>1, the constant is 420420.0 kJ/mol/nm^2. The angle constant for type 1</span></p>
<p><span class=rvts12>is 659.346 kJ/mol/rad2 (776.923 kJ/mol for type 2). Note that you</span></p>
<p><span class=rvts12>can't really obtain one constant from the other, angular functions</span></p>
<p><span class=rvts12>here for small angles are a matter of using Taylor expansion for the</span></p>
<p><span class=rvts12>original potential from solid-state physics. Finally, for</span></p>
<p><span class=rvts12>dihedrals (type 3), the constant is 17.30770 kJ/mol/rad2, so modify</span></p>
<p><span class=rvts12>Andrea's statement to:</span></p>
<p><br></p>
<p><span class=rvts12>C C C C 3 17.30770 0.00000 -17.30770 0.00000 0.00000 0.00000</span></p>
<p><br></p>
<p><span class=rvts12>The types I mentioned are described in Table 5.5 of the GMX</span></p>
<p><span class=rvts12>manual. The reference for the parameters above is my own work: </span><a class=rvts13 href="http://iopscience.iop.org/0957-4484/25/48/485701">http://iopscience.iop.org/0957-4484/25/48/485701</a></p>
<p><span class=rvts12>These are far from perfect (mainly because GMX is a molecular</span></p>
<p><span class=rvts12>mechanics package, so bonds and angles are, well, the simplest</span></p>
<p><span class=rvts12>possible case in mechanics, i.e. springs), but with these values</span></p>
<p><span class=rvts12>they're mathematically guaranteed to reproduce the phonon</span></p>
<p><span class=rvts12>spectrum of graphene/CNTs at 0K. It may not matter for what you're</span></p>
<p><span class=rvts12>doing, but this is at least some level of rigor, because a stable</span></p>
<p><span class=rvts12>lattice isn't actually enough.</span></p>
<p><br></p>
<p><span class=rvts12>2. Make sure you set 'constraints = none' in your mdp. Constraint</span></p>
<p><span class=rvts12>algorithms generally beloved by the biophysical community will turn</span></p>
<p><span class=rvts12>your nanotubes into solid bricks.</span></p>
<p><br></p>
<p><span class=rvts12>Good luck!</span></p>
<p><br></p>
<p><span class=rvts12>Alex</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts12>PB> Hi everyone,</span></p>
<p><br></p>
<p><span class=rvts12>PB> I am new in the Gromacs users community and in the MD field too. However I</span></p>
<p><span class=rvts12>PB> red a lot and I want to realize simulation. I know that it is not trivial</span></p>
<p><span class=rvts12>PB> and that is why I need users help / point of view.</span></p>
<p><br></p>
<p><span class=rvts12>PB> *Project : *Simulate interactions between a single-walled carbon nanotube</span></p>
<p><span class=rvts12>PB> (SWCNT) and a protein.</span></p>
<p><span class=rvts12>PB> (I red tutorials and mailing list archive about this kind of simulation,</span></p>
<p><span class=rvts12>PB> and that is the reason why I come here to find help).</span></p>
<p><br></p>
<p><span class=rvts12>>>>> *Tutorial* : Andrea Minoia (*</span><a class=rvts13 href="http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube?highlight=carbon+nanotube">http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube?highlight=carbon+nanotube</a></p>
<p><span class=rvts12>PB> <</span><a class=rvts13 href="http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube?highlight=carbon+nanotube">http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube?highlight=carbon+nanotube</a><span class=rvts12>>*</span></p>
<p><span class=rvts12>PB> )</span></p>
<p><br></p>
<p><span class=rvts12>PB> *Workflow</span></p>
<p><span class=rvts12>PB> I red manual and utilisation of Gromacs, and that is what I did in</span></p>
<p><span class=rvts12>PB> accordance with Andrea's tutorial :</span></p>
<p><br></p>
<p><span class=rvts12>PB> *#1*</span></p>
<p><br></p>
<p><span class=rvts12>PB> *-- i)* *PDB file of molecules*. For the SWCNT for example. I generated a</span></p>
<p><span class=rvts12>PB> structure from *Nanotube Generator*</span></p>
<p><span class=rvts12>PB> (*</span><a class=rvts13 href="http://www.nanotube.msu.edu/tubeASP/">http://www.nanotube.msu.edu/tubeASP/</a></p>
<p><span class=rvts12>PB> <</span><a class=rvts13 href="http://www.nanotube.msu.edu/tubeASP/">http://www.nanotube.msu.edu/tubeASP/</a><span class=rvts12>>*). From the ".xzy" file generated,</span></p>
<p><span class=rvts12>PB> with Open-Babel (*</span><a class=rvts13 href="http://openbabel.org/wiki/Main_Page">http://openbabel.org/wiki/Main_Page</a></p>
<p><span class=rvts12>PB> <</span><a class=rvts13 href="http://openbabel.org/wiki/Main_Page">http://openbabel.org/wiki/Main_Page</a><span class=rvts12>>*). Then, I generated a ".pdb" file of</span></p>
<p><span class=rvts12>PB> my SWCNT.</span></p>
<p><span class=rvts12>>> COMPLETE.</span></p>
<p><br></p>
<p><span class=rvts12>PB> *-- ii) **Convert in ".gro" format.* With the command :</span></p>
<p><span class=rvts12>PB> """"""""""""""""""""""""""</span></p>
<p><span class=rvts12>PB> editconf -f cnt.pdb -o cnt.gro -box 100 100 100 -angles 90 90 90</span></p>
<p><span class=rvts12>PB> """"""""""""""""""""""""""</span></p>
<p><br></p>
<p><span class=rvts12>PB> I followed advices and made a larger box than nanotube.</span></p>
<p><span class=rvts12>PB> Warning message :</span></p>
<p><span class=rvts12>PB> """"""""""""""""""""""""</span></p>
<p><span class=rvts12>PB> WARNING: all CONECT records are ignored</span></p>
<p><br></p>
<p><span class=rvts12>PB> Read 120 atoms</span></p>
<p><br></p>
<p><span class=rvts12>PB> No velocities found</span></p>
<p><br></p>
<p><span class=rvts12>PB> system size : 0.783 0.783 1.136 (nm)</span></p>
<p><br></p>
<p><span class=rvts12>PB> center : 0.000 -0.000 0.568 (nm)</span></p>
<p><br></p>
<p><span class=rvts12>PB> box vectors : 0.000 0.000 0.000 (nm)</span></p>
<p><br></p>
<p><span class=rvts12>PB> box angles : 0.00 0.00 0.00 (degrees)</span></p>
<p><br></p>
<p><span class=rvts12>PB> box volume : 0.00 (nm^3)</span></p>
<p><br></p>
<p><span class=rvts12>PB> shift : 50.000 50.000 49.432 (nm)</span></p>
<p><br></p>
<p><span class=rvts12>PB> new center : 50.000 50.000 50.000 (nm)</span></p>
<p><br></p>
<p><span class=rvts12>PB> new box vectors :100.000100.000100.000 (nm)</span></p>
<p><br></p>
<p><span class=rvts12>PB> new box angles : 90.00 90.00 90.00 (degrees)</span></p>
<p><br></p>
<p><span class=rvts12>PB> new box volume :1000000.00 (nm^3)</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts12>PB> Back Off! I just backed up new_cnt.gro to ./#new_cnt.gro.2#</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts12>PB> gcq#394: "Restraint! What possible restraint?" (Joseph Conrad)</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts12>PB> So, I think that, I have my atoms but not the connectivity information.</span></p>
<p><span class=rvts12>PB> What should I do?</span></p>
<p><br></p>
<p><span class=rvts12>PB> Because I think that, I have a ".gro" file. But the x2top command send an</span></p>
<p><span class=rvts12>PB> error message : "Segmentation Fault"... And this error is in relation with</span></p>
<p><span class=rvts12>PB> this warning, right?</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts12>PB> This is the first problem.</span></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><span class=rvts12>PB> *#2*</span></p>
<p><br></p>
<p><span class=rvts12>PB> Then, the force field for SWNT.</span></p>
<p><br></p>
<p><span class=rvts12>PB> I red that, I need to edit a force field for the SWCNT to describe</span></p>
<p><span class=rvts12>PB> the behavior of each atoms of this molecule. So, I found that parameters</span></p>
<p><span class=rvts12>PB> what I have to change (Epsilon and sigma of VdW forces, dihedral angles</span></p>
<p><span class=rvts12>PB> etc...). The best way to do this, is to copy "oplsaa.ff" in the current</span></p>
<p><span class=rvts12>PB> repertory and then modify this new force field. And then, use x2top with</span></p>
<p><span class=rvts12>PB> *-ff* option to use the new force field repertory edited few minutes ago.</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts12>PB> This is the right way? (I can not try it because the first step with</span></p>
<p><span class=rvts12>PB> editconf does not work at this moment).</span></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><span class=rvts12>PB> Thanks a lot for your help and time!</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts12>PB> Sincerely,</span></p>
<p><br></p>
<p><span class=rvts12>PB> Pierre.</span></p>
<p><br></p>
<p><span class=rvts12>PB> ?Ps : Second post, I used wrong mailing list address.?</span></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><span class=rvts12>PB> *Pierre BERTIN*</span></p>
<p><span class=rvts12>PB> Bioinformatics and Biostatistics student (MSc),</span></p>
<p><span class=rvts12>PB> University Paris-Sud XI, ORSAY.</span></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><span class=rvts14>--</span></p>
<p><span class=rvts14>Gromacs Users mailing list</span></p>
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<p><span class=rvts15>-- </span></p>
<p><span class=rvts15>Best regards,</span></p>
<p><span class=rvts15> Alex </span><a class=rvts16 href="mailto:nedomacho@gmail.com">mailto:nedomacho@gmail.com</a></p>
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