[gmx-users] Question about ffamber in Gromacs

[Mark Abraham]

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