[gmx-users] free energy

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed May 4 19:01:26 CEST 2011

Dear Gavin:

I'm not seeing a lot of effort on your part to answer these questions.  
I suspect that you can answer some of this. Good luck!


-- original message --

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.


chris.neale at 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

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