Christopher Stiles' Page

~Christopher Stiles

College of Nanoscale Science and Engineering (CNSE)

State University of New York, Albany, New York 12203, USA

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I started with SWNT_6_6_144.pdb and it came from http://turin.nss.udel.edu/research/tubegenonline.html using the following setup:

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Must have the following files in the working directory to start:

SWNT_6_6_144.pdb
ffgmx.n2t

**** must change this files name to ffencadv.n2t and add the following 2 lines:

C C 1 C ; CNT Carbon with one bond
C C 2 C C ; CNT double bonded Carbon
***This addition was only to get the x2top to generate a topology correctly!

ffgmxbon.itp

add the following line to it:
*** To be very clear about this the first two lines are just telling what section to add it to in the file and what the units of that addition reprsent.***

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[ bondtypes ]
; i j func b0 kb
C C 1 0.14210 478900.
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[ angletypes ]
; i j k func th0 cth
C C C 1 120.000 397.480
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[ dihedraltypes ]
; i l func q0 cq
C C 1 0.000 167.360
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*** you can find copies of both of these files at the following location:

/usr/local/gromacs/share/gromacs/top/

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Then using a the following command to generate a topology file from the pdb file:

x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp

During this I chose: 9: Encad all-atom force field, using scaled-down vacuum charges

This gives the following file: SWNT_6_6_144.top

****NOTE: this command never gives a rtp file****

I am not sure why it does not give one

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Next I use the following command to generate the *.gro file and to expand the box 1.0 nm at each all and keep the CNT centered:

editconf -f SWNT_6_6_144.pdb -o SWNT_6_6_144.gro -d 1.0

It creates the following file: SWNT_6_6_144.gro

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Then I use the following command to solvate the box and update the *.gro and *.top file:

genbox -cp SWNT_6_6_144.gro -cs -o SWNT_6_6_144_b4em.gro -p SWNT_6_6_144.top -maxsol 804

It creates the following files: SWNT_6_6_144_b4em.gro SWNT_6_6_144.top

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Then I addaped an *.mdp file form on of the tutorials just to get started. Note I did used the following command on my system:

Which cpp
To get the following output:
/usr/bin/cpp

And I have used both
cpp = cpp
and
cpp = /usr/bin/cpp

!!!!!!!!!!!!!Also Note that it is unix formatted and not edited in windows or dos!!!!!!!!!!!!!!!!!!!

The *.mdp file I use is the following: md.mdp

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Next we must change the SWNT_6_6_144.top file in the following way:

At the top of the file you will see an includes section that looks like this:

; Include forcefield parameters
#include "ffencadv.itp"

Change it to the following:

; Include forcefield parameters
#include "ffgmx.itp"
#include "spc.itp"

Then you must make a copy of the the following files:

ffgmx.itp
spc.itp

from: /usr/local/gromacs/share/gromacs/top/

Then you must copy ffencadv.n2t and rename the copy to ffgmx.n2t

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Next use the following command to make the *.tpr file to run the simulation:

grompp -f md.mdp -c SWNT_6_6_144_b4em.gro -p SWNT_6_6_144.top -maxwarn 10 -pp

Grompp also gives the following output file: mdout.mdp

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Then I use the following to run the simulation:

/usr/bin/time mdrun -s topol.tpr

The first part /usr/bin/time has nothing to do with gromacs

The compleation of this program creates the folowing files:
confout.gro
ener.edr
md.log
traj.trr

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