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]. > -- 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].
