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
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