[gmx-users] CNT force field and simulation

Pierre Bertin bertinp71 at gmail.com
Sat Apr 11 21:02:32 CEST 2015

Hi everyone,

I am new in the Gromacs users community and in the MD field too. However I
red a lot and I want to realize simulation. I know that it is not trivial
and that is why I need users help / point of view.

*Project : *Simulate interactions between a single-walled carbon nanotube
(SWCNT) and a protein.
(I red tutorials and mailing list archive about this kind of simulation,
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

*Workflow :*
I red manual and utilisation of Gromacs, and that is what I did in
accordance with Andrea's tutorial :


*-- i)* *PDB file of molecules*. For the SWCNT for example. I generated a
structure from *Nanotube Generator* (*http://www.nanotube.msu.edu/tubeASP/
<http://www.nanotube.msu.edu/tubeASP/>*). From the ".xzy" file generated,
with Open-Babel (*http://openbabel.org/wiki/Main_Page
<http://openbabel.org/wiki/Main_Page>*). Then, I generated a ".pdb" file of

*-- ii) **Convert in ".gro" format.* With the command :
editconf -f cnt.pdb -o cnt.gro -box 100 100 100 -angles 90 90 90

I followed advices and made a larger box than nanotube.
Warning message :
WARNING: all CONECT records are ignored

Read 120 atoms

No velocities found

    system size :  0.783  0.783  1.136 (nm)

    center      :  0.000 -0.000  0.568 (nm)

    box vectors :  0.000  0.000  0.000 (nm)

    box angles  :   0.00   0.00   0.00 (degrees)

    box volume  :   0.00               (nm^3)

    shift       : 50.000 50.000 49.432 (nm)

new center      : 50.000 50.000 50.000 (nm)

new box vectors :100.000100.000100.000 (nm)

new box angles  :  90.00  90.00  90.00 (degrees)

new box volume  :1000000.00               (nm^3)

Back Off! I just backed up new_cnt.gro to ./#new_cnt.gro.2#

gcq#394: "Restraint! What possible restraint?" (Joseph Conrad)

So, I think that, I have my atoms but not the connectivity information.
What should I do?

Because I think that, I have a ".gro" file. But the x2top command send an
error message : "Segmentation Fault"... And this error is in relation with
this warning, right?

This is the first problem.


Then, the force field for SWNT.

I red that, I need to edit a force field for the SWCNT to describe
the behavior of each atoms of this molecule. So, I found that parameters
what I have to change (Epsilon and sigma of VdW forces, dihedral angles
etc...). The best way to do this, is to copy "oplsaa.ff" in the current
repertory and then modify this new force field. And then, use x2top with
*-ff* option to use the new force field repertory edited few minutes ago.

This is the right way? (I can not try it because the first step with
editconf does not work at this moment).

Thanks a lot for your help and time!



​Ps : Second post, I used wrong mailing list address.​

*Pierre BERTIN*
Bioinformatics and Biostatistics student (MSc),
University Paris-Sud XI, ORSAY.

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