IF it's NVT, then you should just be able to add harmonic potentials using the position restraints (not constraints) -- the harmonic restraints can be controlled by lambda. You should only need to alter the charge and VDW interactions -- no need to adjust the bonds.
We have been doing some work on crystals of small organics-- email me off the list and we might be able to give you some example scripts. On Fri, Dec 11, 2015 at 8:46 PM, Nathan K Houtz <nho...@purdue.edu> wrote: > Hello, > > > I would like to perform some free energy calculations of ice Ic (cubic ice) > at various temperatures. However, I'm having difficulty finding information > on how Gromacs can be used to do this. The goal is to gradually turn off VDW > and Coulomb interactions, just as one would do in a liquid, but also turn on > virtual spring-like potentials to create an Einstein crystal, which is where > I'm having trouble. I know you can fix atom locations, and considering bond > potentials are spring-like, my best idea is to create a virtual copy of each > molecule (not virtual sites, but just atoms that have no charge and don't > interact with other atoms/molecules), fix it in the crystal lattice, and > create bonds between corresponding atoms with an equilibrium distance of 0. > But this means I have to simulate twice as many atoms, and more importantly I > don't know how to couple only some of a molecule's bonds with lambda. Am I > even on the right track, or is there a more straightforward way to do this? Ar > e there any tutorials for free energies of solids that I could take a look > at? (I couldn't find any) > > > Thanks for your help! > > N. H. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
