[gmx-users] Simulating Infinite Nanotube

Robert Johnson bobjohnson1981 at gmail.com
Thu Nov 1 21:55:41 CET 2007

Are you absolutely sure that the terminal carbon atoms are sharing a
bond in the topology file? Make sure of this. If they really ARE
bonded within the topology file, then I don't think the crumpling is
due to Gromacs incorrectly reading the topology (by the way, use
pbc=full). Provided that the topology file is correct, the crumpling
may be due to placing the nanotube in a box of wrong dimension. Use
VMD to visualize the nanotube and its periodic images and make sure
that the space between images is correct. If the spacing is too small
or too big, there will be a large amount of stress induced in the tube
which will lead to crumpling or stretching. Don't apply pressure
coupling along the axis of the nanotube. In fact, for debugging
purposes, it might be better to turn off pressure coupling altogether
until you figure out what's going wrong.

On Nov 1, 2007 3:29 PM, Patrick Lafond <patlafond at gmail.com> wrote:
> Hello, I was wondering if perhaps someone could help me out with running a
> simulation of an infinite CNT.  I have searched through the archives before
> and have tried all of the suggestions I was able to find but still can't
> seem to figure out what the problem is so I decided it best to try and ask
> for direct help.  Here is what I have done:
>      1) Taken the PDB file which is exactly the structure for the tube and
> converted it to a gro file with the proper dimensions for periodic height
> and ample room on the sides.
>      2) Used x2top to convert the gro file to a topology file using the
> "-pbc" option.  In the topology file I see that it is infact specifying
> bonds between the carbons at the top of the tube and carbons at the bottom
> of the tube.
>      3) I have tried running the simulation using different options for the
> pbc in the mdp file.  I at first tried pbc = xyz but then changed that to
> full.  I also tried fiddling with
> non-bonded exclusion trying 3, 4, and 5.  I also tried changing the time
> steps to shorter steps.
>      4) When none of the above mentioned attempts seemed to work I tried
> making a new slightly shorter tube using the same method mentioned above.
>      Regardless of what I seem to do every time the simulation yields the
> same results which is that it won't run.  LINCS provides a warning for just
> about every carbon in the tube a handful of times and then reports that
> there were errors in the simulation.  Upon reviewing what it had
> accomplished the ends of the tube, and 2 rows in the very middle of the tube
> crumple together and them fly apart presumably from how close together the
> atoms are forced there.  I have a very strong suspicion that the simulation
> isn't recognizing that the atoms are actually bonded to atoms in the image
> (which would explain the crumpling from how close the atoms are to the
> periodic image) but cannot figure out how to actually achieve this
> recognition in the simulation.  I read just recently that LINCS has problems
> with molecules containing a lot of bonds but then read the problem is more
> with the constraints applied.  It doesn't seem like the error is in LINCS
> rather it is a lack of recognition of bonding between the actual molecule
> and the image.  Thanks for your time, I hope I can get some help on this.
> (By the way, I am running the simulation on version 3.1.1 if that might
> account for any of the problems)
> Sincerely,
> Patrick
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