[gmx-users] a gromacs feature to do TMD like simulation

[michael.b]

did you look at the documentation for the pull code?

generally you want to be careful interpreting such calculations ... the
parameters for commonly used
protein force fields were fitted to reproduce equilibrium structures ...
even if they were, in principle,
applicable to what's in between (transition state geometries) this would
still leave the problem
that in most cases the structures of such transition states are poorly
defined. In particular for
a transition involving an extensive rearrangement of a protein loop there is
a myriad of 
potential pathways to go from one equilibrium state to another, and you'd
have to obtain a
thorough sampling of these pathways to get a meaningful answer to your
question - this
might turn out prohibitive in view of the required simulation times ...

cheers
mic


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