Hi GMX-users,
I am beginning to use the steered molecular dynamics method to perform a
potential of mean field calculation. In your experience, does it matter what
kind of a thermostat and pressure coupling is used? Does Nose-Hoover and
Parinello-Rahman perform better than Berendsen for this purpose? Does it even
matter?
Also with regards to the constraints on the bonds using the "all-bonds" option,
Does it matter? I worry that applying constraints on the molecule being pulled
will prevent it from sampling the configurational space effectively and thus
giving false results on the PMF and binding energies. Maybe I am completely off
the mark here.
Thanks in advance.
Regards
Rama
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