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