Hi :) I'd say that if the changes are small you should be able to get away with it. You might want to start off the second part of the run with a smaller time step to relax, though. If the change is from TRP to TRP*, you only need to have a modified topology, without touching the coordinates. You do need to set up a new .tpr file from the the .trr and the modified topology.
Hope it helps, Tsjerk On Tue, Mar 15, 2011 at 10:11 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > J. Nathan Scott wrote: >> >> Hello all, >> >> I was wondering, is it possible to replace a residue and then continue >> a simulation using the new parameters/geometry of the new residue? The >> reason I ask is that I am interested in performing simulations of >> proteins with tryptophan in its excited state following a lengthy >> equilibration with TRP in its ground state. I already have reliable >> excited state atomic charges for the TRP atoms, and I suppose that I >> will need to change at least some bonded terms to account for the >> altered geometry of the excited state. >> >> I am still in the middle of reading the information that is out there >> regarding parameterizing new molecules (since I'm using the CHARMM FF, >> I've been starting to follow Alexander MacKerell's protocols), but I'm >> still not quite sure as to how one would practically do this residue >> replacement in the context of a Gromacs run. Will I need to manually >> edit my .top file, or is there perhaps another way to update the >> topology file with the new residue following the ground state >> equilibration? How about coordinates, will I need to transform the TRP >> coordinates to the excited state geometry by hand? >> > > You would have to hack the topology. Coordinates are another matter. If > you start making ad hoc changes, then what's the point of a continuation? > Presumably, if you've designed the residue's topology correctly (including > both bonded and nonbonded parameters), then the residue will adopt the > correct geometry on its own. > > The complication comes with bonded interactions. Are you using constraints? > If so, then changing bond lengths will cause the constraints to fail at > step 0 (or very soon thereafter) and the simulation will crash. You can get > around this by setting "continuation = no" in the .mdp file, but again I > wonder what the value of the continuation is. You'd almost certainly have > to forgo the use of .cpt files, supplying instead your .trr and .edr files > to preserve as much of the previous ensemble as possible. Even if you're > not using constraints, the simulation may still fail if you're suddenly > changing bond lengths, angles, etc by anything more than a very small > amount. > >> Perhaps the most important question: is there a better way to do the >> sort of residue replacement I'm contemplating, or is this something >> that is just inherently going to be a bit messy? >> > > I can't see any way around topology hacking. If you need different > parameters, you need a different topology. It's going to be a bit messy, > and I would encourage you to give some serious thought to the potential > pitfalls I listed above. > > -Justin > >> Thanks very much for any insight or guidance you can offer! >> > > -- > ======================================== > > 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 > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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
