Thanks for taking the time to answer, but I think my wording may have confused my question. I shouldn't have used the word box. Within the protein their are several aromatic residues that interact with the small molecule cation. I would like to preserve these interactions throughout the simulations. Is it possible to "enhance" these interactions, since there is no defined force constants that describes these interactions? Thanks. Egy
On Oct 24, 2011, at 12:19 PM, Justin A. Lemkul wrote: > > > EGY wrote: >> I am interesting in modeling a small molecule ligand-protein complex that >> involves a cationic ligand encapsulated by several aromatic residues that >> form a box around the cation. However, md simulations result in the cation >> moving outside the box. I am using the CHARMM27 forcefield. Is there a way >> to restrain the cation portion of the small molecule to within the aromatic >> box? Or is there a better forcefield, which will take these interactions >> into consideration. > > More than likely you simply need to account for periodicity. > > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > > -Justin > >> Thanks. >> Egy-- 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 > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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
