[gmx-users] How to make carbon nanotube infinite?

[Justin A. Lemkul]

Cun Zhang wrote:

<snip>

> I mean, I make  the distance of the top ( or bottom ) C atoms in CNT and 
> the corresponding edge of the box equals the length of a C-C bond( about 
> 0.142nm ).

OK, that sounds reasonable, but did you define the periodic bonds appropriately? 
  Your original question was that you did not know how to do that.

> I use a (16,0) CNT with 832 atoms ( length 5.472nm).I use the following 
> command to produce a CNT-water system
> 
>  >editconf -f CNT.pdb -o -box 3.8 3.8 5.614
> 
> No velocities found
>     system size :  1.270  1.270  5.472 (nm)
>     center      : -0.000  0.000  2.736 (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       :  1.900  1.900  0.071 (nm)
> new center      :  1.900  1.900  2.807 (nm)
> new box vectors :  3.800  3.800  5.614 (nm)
> new box angles  :  90.00  90.00  90.00 (degrees)
> new box volume  :  81.07               (nm^3)
> 
>  >genbox -cp out -cs -p CNT -o b4em.pdb
> 
> Output configuration contains 7513 atoms in 2228 residues
> Volume                 :     81.0662 (nm^3)
> Density                :     1026.51 (g/l)
> Number of SOL molecules:   2227  
> 
> Processing topology
> Adding line for 2227 solvent molecules to topology file (CNT.top)
> 
>  >pymol b4em.pdb # I write a python script to remove the SOL molecules 
> in the Carbon nanotube.

Are there any solvent molecules interfering with the cross-boundary bonds?

>  >editconf -f b4em.pdb -o b4em.gro -box 3.8 3.8 5.614 #rebuild the box.

Why are you doing this?

>  >grompp -v -f em -c b4em -o em -p CNT -maxwarn 5

Are there warnings you are ignoring by using -maxwarn 5?

> NOTE 1 [file CNT.top, line unknown]:
>   The largest charge group contains 32 atoms.
>   Since atoms only see each other when the centers of geometry of the charge
>   groups they belong to are within the cut-off distance, too large charge
>   groups can lead to serious cut-off artifacts.
>   For efficiency and accuracy, charge group should consist of a few atoms.
>   For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
> 

Pay attention to this note.  A charge group of 32 atoms is huge.

> 
> Checking consistency between energy and charge groups...
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 32x32x48, spacing 0.119 0.119 0.117
> Estimate for the relative computational load of the PME mesh part: 0.41
> This run will generate roughly 15 Mb of data
> writing run input file...
> 
> There was 1 note
> 
> Back Off! I just backed up em.tpr to ./#em.tpr.1#
> 
> gcq#87: "It's Because Of the Metric System" (Pulp Fiction)
> 
>  >mdrun -v -s em
> Back Off! I just backed up md.log to ./#md.log.1#
> Getting Loaded...
> Reading file em.tpr, VERSION 4.0.5 (single precision)
> Loaded with Money
> 
> 

OK, so what happens?  Does the EM converge, or does the minimization fail?

> Back Off! I just backed up traj.trr to ./#traj.trr.1#
> 
> Back Off! I just backed up traj.xtc to ./#traj.xtc.1#
> 
> Back Off! I just backed up ener.edr to ./#ener.edr.1#
> starting mdrun 'CNT in water'
> 50000 steps,     25.0 ps.
> step 0Segmentation fault
> 

Instant crashing indicates the structure is unstable, and that EM likely wasn't 
sufficient.

> THE b4em.gro file is like:

There is no useful information in the .gro file, and nothing out of the ordinary 
in the .mdp file.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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