> Hello all, > > I am new to using Gromacs and MD simulation. I am simulating a 9-residue > drug with a box of water. I generated the box using this: > editconf -f xx.gro -o xx.gro -d 0.5 -bt cubic > > everything seems fine and the MD run went smooth. However when I look at > the trajectory, I see that the drug goes of the water box and the > simulation ends up with the drug attached to the outside of the box. > > Does this mean that I should increase the size of my box? > before running the md, the drug was centered into the box of water molecules. > > I appreciate any help. > Thank you > > Belquis Mothana
There are a number of threads in the mailing list archive about this. A fairly recent one can be found at: http://www.gromacs.org/pipermail/gmx-users/2007-February/025797.html I believe that deals with a similar problem, based on what you've described. If you're applying periodic boundary conditions (pbc = xyz) in your .mdp file, then there shouldn't be anything wrong with the simulation. Search the archives for more information. Best of luck, 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
