[gmx-users] Monte Carlo with Gromacs and implicit solvent
Mark.Abraham at anu.edu.au
Tue Jan 24 10:24:01 CET 2012
On 24/01/2012 12:39 PM, Gianluca Interlandi wrote:
> I would like to use gromacs to perform Monte Carlo simulations in
> implicit solvent of a protein near a surface. The protein is treated
> as a rigid body whereas the surface is fix.
> I see that there are plans to code MC into gromacs:
> Is there a preliminary version?
> If not, I wonder whether anybody has tried to do MC with gromacs using
> IMD and MDDriver:
> Besides this. Is there an easy way to obtain the force field energy of
> a system using gromacs? Would I have to run a 0-steps MD and read out
> the energy? I know that this would have a big overhead in a MC
> simulation, but it might be worth trying.
Since the topology is constant over the simulation, scripting mdrun
-rerun on a string of potential trial moves is a reasonably efficient
way to produce a draft version of your algorithm.
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