The current simulations are currently in vacuum. Does the following mdp file seem ok. Note that this is a production run using the final configuration after a lengthy equilibration. Also I was thinking about trying to prevent the other chains from entering the specific site; is there a a way to implement this in gromacs.
Gavin chris.ne...@utoronto.ca wrote: > yes it will, and so will it affect the profile if water molecules or > ions go in when both chains are absent. > > You'll need to determine what question you are trying to answer and > also think pretty hard about what your PMF really means in the context > of this system. > > Chris. > > -- original message -- > > > Hi Chris > > My windows are restrained obviously using the force constant in the mdp > file. The trajectories that I have viewed are those of the individual > biased sampling windows. I have not put on the unbiased simulations yet. > There is also the following issue: The simulations involve two identical > molecules containing hydrocarbon chains. I calculate the PMF to take a > specific hydrocarbon chain of one molecule out of a specific site on the > neighbouring molecule. When this guest chain goes out, other chains can > go in (intramolecular or intermolecular). Will this affect the profile? > > Gavin > >
umbrella81.mdp
Description: application/mdp
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