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

Justin A. Lemkul jalemkul at vt.edu
Wed Nov 25 02:58:03 CET 2009

Cun Zhang wrote:


> I hope generate sharing bonds between the atoms at the top edge and the 
> atoms at the bottom edge of CNT by x2top. But the parameter -pbc does 
> not work. So I add 4 layers at the top of CNT.pdb and rename it 
> CNT_new.pdb, that is, the front 832 rows of them are same. 
> The  atoms of No. 833-960 in CNT_new.pdb can be seen the bottom 4 layers 
> of atoms of No.1-128 of CNT.pdb translated up a box hight. So after 
> generating the topology file and renaming atoms of No. 833-960 to 
> No.1-128 in the topology file (use the command 'x2top -nopbc') the 
> topology file  of CNT_new.pdb should be the same as the topology file of 
> CNT.pdb with sharing bonds (and angles, diherals) ( use the command 
> 'x2top -pbc' ).

This still makes no sense to me at all.  You're creating duplicate atoms at one 
end of the structure to make them have the same atom numbers of those at the 
other end of the molecule?  Forgive my confusion, I simply don't know what 
you're doing.  The concept of bonding is not that parameters are "shared," it is 
the following:

Consider atoms A and Z, residing at the "ends" of a CNT, as shown here (with 
vertical lines indicating the boundaries of the unit cell):

|                   |
| A . . . . . . . Z |
|                   |

You simply need to define a bond in the topology between A and Z, no renumbering 
or fancy tricks required, just add the bond to the [bonds] directive:

[ bonds ]
A Z 1

That gives the following:

|                   |
|-A . . . . . . . Z-|
|                   |

This bond then spans the periodic boundary.

I'm surprised the EM worked, but I am still unclear on your approach thus far.


> 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.

These notes are not simply printed for your entertainment.  If you have a 
32-atom charge group, you will have potentially severe artifacts, especially if 
you are using cutoff electrostatics, which you are (see additional comments 
below).  Please read in the manual about how to properly define charge groups.


> NOTE 2 [file em.mdp, line unknown]:
>   You are using a plain Coulomb cut-off, which might produce artifacts.
>   You might want to consider using PME electrostatics.

Again, heed the note.  I cannot think of a solid reason for a modern simulation 
being conducted using cutoff electrostatics, unless the goal is to prove that 
such a method is less accurate than a more modern technique like PME.  Again, 
these notes are your friend.  I see that they return during your PR attempts. 
You should not ignore the advice that grompp is giving you.  The artifacts of 
plain cutoffs are well-documented.

Several other resources to consider using:





Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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