You can try a run in implicit solvent to get a feel for the maximum diameter of the protein while unfolding. You will not have any certainty unless you can afford a box whose diameter is that of the straight-line peptide...
Mark On Sat, Sep 21, 2013 at 1:03 PM, aksharma <arunsharma_...@yahoo.com> wrote: > 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 -- 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
