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

[Cun Zhang]

hi, Justin. Thank you for your patience !

I'm still in trouble with infinite CNT simulation.

I'm trying to simulate the interaction of  a infinite (16,0) CNT(CNT_A) with
832 atoms and water. I'm using x2top to generate the CNT.itp with
share-bonds. The idea is that I generate a (16,0) CNT(CNT_B) with 960 atoms
( more 4 layer  than CNT_A. Each layer has 32 atoms ).
When I use CNT.itp generated by  CNT_A and x2top, it works. But when I use
the CNT.itp which has share-bonds information, it can't work.


The process I'm doing CNT simulation is as follows:
# the CNT_new.pdb is a (16,0) CNT with 960 atoms.
# I add the custom forcefield parameters to tmp.top, and change the number
of a charge group to 32, then rename it CNT.itp at the end.

x2top -f CNT_new.pdb -o tmp.top -ff gmx -nopbc -nopairs -noparam -name CNT


bash sharebond_script   # create share bonds

editconf -f CNT.pdb -o -box 3.8 3.8 5.614

genbox -cp out -cs -p CNT -o b4em.pdb  #The simulation box size can be seen
in b4em.pdb

pymol b4em.pdb  #remove water. After editing it,I save it as b4em.pdb
too.Now the information about box size is losing. I don't know why.I'm not
familar with it :)

editconf -f b4em.pdb -o b4em -box 3.8 3.8 5.614 # Add the information about
box size
vim CNT.top     #change the number of water to make it the same as b4em.pdb
grompp -f em -o em -c b4em -p CNT -maxwarn 5
mpirun -np 4 mdrun_mpi -v -s em -e em -o em -c after_em
grompp -f grompp -o pr -c after_em -p CNT -maxwarn 5
mpirun -np 4 mdrun_mpi -v -s pr -e pr -o pr -c after_pr

The sharebond_scrip code:

#!/bin/bash
sed -e '/^ *83[3-9].*UNK/d' -e '/^ *8[4-9][0-9].*UNK/d' -e '/^
*9[0-9][0-9].*UNK/d'  CNT.itp >tmp # remove the atoms whose number is larger
than 832 in [ atoms ].
for((i=833;i<=960;i=i+1))   # change the number(i) of atoms which is larger
than 832 to i-832.
do
    j=$((i-832))
    N=$((3-${#j}))
    L='   '
    j=${L:1:N}$j
    sed -i "s/ $i / $j /" tmp
done
awk '!a[$0]++' tmp>CNT.itp # make the CNT.itp file have no repetitive rows

I upload a log file for more information in there (
http://4message.net/blog/wp-content/uploads/2009/11/CNT.tar.bz2 )

Cun Zhang wrote:
> > Hi, Justin.
> > Thank you for your help! I was intended to reply the third question
> > after I retryed the simulation under your advice,but I haven't enough
> time
> > to do it. It's too late :)
> >
> > Just now, I do a simulation. All seems ok. I will check it again.
> >
> > Thank you again!
> >
> > Cun Zhang
> >
> >      >  >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?
> >
> >
> > No.I use pymol to remove all residues which is far from the egdes 0.7A .
> >
> >
>
> OK.
>
> >
> >      >  >editconf -f b4em.pdb -o b4em.gro -box 3.8 3.8 5.614 #rebuild
> >     the box.
> >
> >     Why are you doing this?
> >
> >
> > The b4em.pdb generated by genbox have no information about box size. So
> > I use editconf to generate it.
> >
>
> That is not true.  Gromacs can handle a number of coordinate file types,
> and box
> dimensions are written to the CRYST1 line in the .pdb file.  You should
> never
> have to re-define your box unless you are doing some very advanced
> manipulations
> (which you are not, in the case of simply solvating a structure).
>
> >      > 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.
> >
> >
> > So what's your suggestion about the number of a charge group?
> >
>
> The note from grompp is quite detailed, and even gives examples of
> appropriate
> charge group sizes.
>
> -Justin
>
> >
> > --
> > Blog: http://blog.4message.net
>
> --
> ========================================
>
> 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
>




-- 
Blog: http://blog.4message.net
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