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

[quantrum75]

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



      
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100929/ffa026c5/attachment.html>