bo yang wrote:
Dear gromacs user,
I am doing the MD simulation of CNT-DNA interaction.
Before introducing DNA, I used gromacs default force field
and finished the simulation of CNT (carbon nanotube). And,
in the ffgmxnb.itp , I introduced the non-bonded parameters
for C-C and C-OW (oxygen) in the [non-bonded param] session.
Now, I have the amber99 package. I opened ffamber99nb.itp and
compared the format of ffamber99nb.itp to ffgmxnb.itp.
There is only [atoms] session in ffamber99nb.itp.
Do you mind telling me how to introduce these non-bonded
parameters (L-J parameters) for C-C and C-OW in ffamber?
Do I just simply add [non-bonded param] at the end of the ffamber99nb.itp
and list the parameters there?
Rather than editing the standard files, you should create a new file
with all the stuff for your CNT and #include it
(http://wiki.gromacs.org/index.php/include_file_mechanism). You can have
multiple [non-bonded param] sections, IIRC. Read chapter five of the
manual carefully.
Of course, you've found a literature source that recommends mixing the
same CNT parameters with two different DNA force fields? See
http://wiki.gromacs.org/index.php/Parameterization for why this is a bad
idea.
I guess this is important for me because I attempted to add [non-bonded
param]
at the end of the itp file. After the energy minimization, I visualized
that the
carbon nanotube is standing above the simulation box.
I bet this is the usual non-problem mentioned here
http://wiki.gromacs.org/index.php/Periodic_Boundary_Condition
Also, I realize that the atom mass in ffamberXX.itp is 0, but in
ffamberXX.atp,
all masses are non-zero. Do you minding explain it for me in detail?
This got explained in reply to the last time you asked this question.
Please read people's replies. How come I can remember the answer that
someone gave their time freely to provide, when the person who asked it
doesn't remember there was an answer?
Mark
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