[gmx-users] periodic carbon nanotubes

Andrea Minoia minoiaa at gmail.com
Sat Dec 5 20:29:31 CET 2009

Hi there,
I'm back to gromacs after some time and I'm trying to build a periodic single wall armchair nanotube with gromacs 4.0.5.  
I decided to start from scratch, writing my own set of .atp, .rtp, itp files based on oplsaa forcefield, as I was used to do before for polymers.
I have already red the CNT how-to on the wiki and followed Robert's tips (except for x2top which I was not able to use), visited Christopher's website (but his nanotube does not seem to be periodic) and had a look at the mailing list (something came out about infinite polymers).

I have generated without errors the topology file using pdb2gmx and manually added all the sharing bonds, angles and torsions that cross the periodic cell. Since my nanotube is periodic along the Y-axis, I have adjusted the size of the cell for Y and increased to 10 the value for the X and Z axes, so to have a "single" nanotube. Checking with vmd, the bonds crossing the unit cell have the right value of 1.42 angstrom, and also angle and dihedrals seems to be corrected.

I have turned on the periodic_molecules and set pbc = xyz in the .mdp file. Pressure coupling is off and bonds are not constrained. As you can see below, I was able to generate a valid .tpr file with grompp:

==== grompp -c cnt.gro -p cnt.top -f grompp.mdp ====
checking consistency between energy and charge groups...
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 90x7x90, spacing 0.119 0.105 0.119
Estimate for the relative computational load of the PME mesh part: 0.96

NOTE 1 [file aminoacids.dat, line 1]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing

This run will generate roughly 2 Mb of data
writing run input file...

There was 1 note

To test all, I decided to use the steep algorithm, but when I run mdrun I got segmentation fault:

==== mdrun -v -c cnt.gro ======
Back Off! I just backed up md.log to ./#md.log.1#
Getting Loaded...
Reading file topol.tpr, VERSION 4.0.5 (single precision)
Loaded with Money

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+01
   Number of steps    =       100000
Step=    0, Dmax= 1.0e-02 nm, Epot=  1.38163e+03 Fmax= 8.83426e+02, atom= 23
Segmentation fault

md.log does not really tell something to me. 

I have also try to remove all the pairs, exclude them and set to zero angle and dihedral potential (I do not have impropers at the moment). Nothing seems to improve the situation.
I'm wondering if I have misunderstood the use of periodic_molecules: does the molecule need to be periodic in the 3 X- Y- Z- directions or it can be periodic just along one directions, as in the case of CNT?

Any help is more appreciated.

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