[gmx-users] Re: Nitrogen box

sarah k dailycolors at gmail.com
Tue Mar 1 08:18:05 CET 2011

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

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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