[gmx-users] Free energy of ice crystals (Thermodynamic Integration)

Michael Shirts mrshirts at gmail.com
Sat Dec 12 05:06:31 CET 2015

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 <nhoutz at 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.
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