Hi Justin, Thanks for your reply. I have some follow-up questions. Since the simulation is high temperature (450 K) there is slight unfolding of the protein.
The box was set up as rhombic dodecahedron with 1.2 nm as the distance between solute and edge of box. pdb2gmx -f 1L2Y.pdb -o 1L2Y-processed.gro -ignh -water spce The cutoffs are 0.9 nm for VDW and electrostatics. Do you suggest using an even bigger box for studying unfolding? Or is there something else that could be going on? Do you have any ball park suggestions for a good size of the box or is this something that I would have to experiment with different sizes until I land a suitable box. Thanks a lot, -- View this message in context: http://gromacs.5086.x6.nabble.com/Minimum-distance-periodic-images-protein-simulation-tp5011343p5011347.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
