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 _______________________________________________ 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
