Hi, For a tutorial and a workflow you can also check out:
http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/ http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/01-Preparation-Workflow.jpg A bit in progress still, and any comments welcome ;) Cheers, Tsjerk On Sat, Jun 21, 2008 at 9:40 AM, Vitaly Chaban <[EMAIL PROTECTED]> wrote: >> 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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
