--- [EMAIL PROTECTED] wrote:
> Dear Gromacs community. > > I am just starting my first dynamics and wonder if > you could help me with: > > 1. Want to use some graphical program to see the > atoms moving. Can I use > ngmx? What other programs are available? Yes, ngmx will work just fine, albeit crudely. VMD is another good option - has reasonably good graphics and analysis features, and lets you convert a trajectory into a movie. There are other trajectory viewing programs out there, but I don't think they can read GROMACS trajectories. > > 2. This is the near the end of my .top file in the > final MD step: > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcx fcy fcz > 1 1 1000 1000 1000 > #endif > > If I want the waters to be free, should I comment > out these lines? I'm pretty sure position restraints only turn on if you specify them to in your .mdp file. You'll notice the first line of your statement contains the word IF. The default is for no PR. Look at the mdp files in the share/tutorial/ folders. > > Thank you, João. > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
