[gmx-users] TMD using free energy code

[Landraille]

Dear Gromacs users,

I would like to perform targeted molecular dynamics with gromacs. I have
read all the post concerning it and I can do it with position restraints by
putting the final conformation in the -r option of grompp.
But this is not a "real TMD". Indeed, in TMD, the force applied to the
structure is dependent of the RMSD in order to have a constant RMSD
decrease. Here the force is constant. So, when the starting conformation is
far from the final conformation the RMSD decreases quickly but when it's
near the final conformation, the force constant can be not enought and the
final conformation can be never reached (unless putting a big force).

I see in the manual in the paragraph 6.4 that it's possible to do TMD with
the free energy options and the -r -and -rb options of grompp. Nevertheless,
none example is available for the mdp input file. How i can do it please?

Thank you

Landraille



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