> Special thanks to Vitaly, Mark and Justin for there comments. I've > revisited the wiki site and read through chapter 5 of the manual. I'm > currently going through the tutorial with a standard protein. I run into a > problem when I use the command: > > grompp -f em.mdp -c fws_b4em.pdb -p fws.top -o fws_em.tpr > > The error states that the em.mdp file doesn't exists, but none of the > steps in the tutorial leading up to this command creates the em.mdp file. > I was just wondering what step in the process is the .mdp file created or > do I have to have that already created off to the side ready for the > grompp command? > > Thanks again, > > -John Landers
I guess em.mdp is a parameter file for energy minimization. Look here: http://www.gromacs.org/documentation/reference/online/mdp.html for how one can make it. If you want to make an energy minimization of your system firstly, you just have to change "integrator = md" to "integrator = l_bfgs" or "integrator = steep" I have also sent you personally the ready example to start with simulating carbon nanotube. Best, Vitaly _______________________________________________ gmx-users mailing list [email protected] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
