[gmx-users] free energy

[Gavin Melaugh]

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.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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