On 03/01/11, sarah k <[email protected]> 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. Mark > 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 > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >
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