[gmx-users] CNT force field and simulation

[Pierre Bertin]

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 <nedomacho at gmail.com>:

> 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.
>
>
>
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