________________________________ From: Adrien Delmont <adriendelm...@yahoo.com> To: jalem...@vt.edu Sent: Wednesday, March 11, 2009 6:09:53 PM Subject: Re: [gmx-users] get a box of 100 molecules I didn't get gro and top files with any force field in Gromacs. I basicly want to use oplsaa and GROMOS96 43a2 force field (improved alkane dihedrals) . I think I should add all the parameters but how can I add my parametes both into oplsaa and GROMOS96 43a2 force field ? Thanks in advance ________________________________ From: Justin A. Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Wednesday, March 11, 2009 5:48:59 PM Subject: Re: [gmx-users] get a box of 100 molecules Adrien Delmont wrote: > /Dear Users, > > I'm new to Gromacs. Before I try to generate a box of 100 molecules, I wanted > to ask it to the users. Can I get a box of 100 molecules that are randomly > //distributed/ /and not attached to each other using the commands below? If > there are something wrong in commands please share your valuable suggestions > with me. Try it and see. > Thanks in advance > /// > Adrien > > pdb2gmx -f mol.pdb -o mol.gro -p mol.top -i mol.itp ( then chose suitable > force field ) > //// This will only work if the force field contains parameters for your molecule. -Justin > //////////genbox////////// //////////-ci////////// mol.gro //////////-nmol > 100//////// //-o 100mol.gro //////-p > 100mol.top//// ////////-box 12 12 12////////// > > // > > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ======================================== Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
