[gmx-users] Monte Carlo with Gromacs and implicit solvent

[Mark Abraham]

On 24/01/2012 12:39 PM, Gianluca Interlandi wrote:
> Hi!
>
> 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:
>
> http://www.gromacs.org/Developer_Zone/Programming_Guide/Monte_Carlo
>
> Is there a preliminary version?
>
> If not, I wonder whether anybody has tried to do MC with gromacs using 
> IMD and MDDriver:
>
> http://www.baaden.ibpc.fr/projects/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.

Mark