[gmx-users] CNT force field and simulation

Alex nedomacho at gmail.com
Sat Apr 11 21:41:43 CEST 2015

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
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!


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> *-- 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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