[gmx-users] Steered molecular dynamics and Parinello-Rahman and bond constraints.

quantrum75 quantrum75 at yahoo.com
Wed Sep 29 21:00:27 CEST 2010

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.

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