[gmx-users] Re: Nitrogen box

Mark Abraham mark.abraham at anu.edu.au
Tue Mar 1 11:10:00 CET 2011

On 03/01/11, sarah k  <dailycolors at gmail.com> wrote:
> Dear Justin,
> Thanks for your reply. Now, I have problem in generationg the
> coordination file. Since my molecule is diatomic, the PRODRG server
> fails and when I used another parametrization tool, the output files
> were void. Can I generate the file in gromacs? Is there any way to do
> it?

I'm not sure what you're asking. Justin suggested a good approach for generating a "solvent box" of nitrogen.

Implementing an MD model of dinitrogen in a .top/.itp file is about 5 minutes' work with a text editor if you already have suitable parameters and an existing .top to act as a template. (One [atomtype], one [bondtype], one [moleculetype], two [atoms], one [bonds]. Then a [molecules] section. Finished.) If you don't have parameters already, search the literature in the first instance.


> Regards,
> Sarah Keshavarz
> > sarah k wrote:
> >> dear users,
> >>
> >> I want to use Nitrogen as my solvent. How can I prepare the box and
> >> compile the *.gro file? Please, guide me in detail. Thanks in advance!
> >>
> >
> > Make a coordinate file for a single N2 molecule (should be really easy) and
> > use
> > either genconf -nbox or genbox -ci -nmol to create the solvent box, then
> > equilibrate.
> >
> > -Justin
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