quantrum75 wrote:
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?
That depends on how rigorously correct you want your ensemble to be. Berendsen
coupling does not generate temperatures/pressures that correspond to any known
statistical mechanical ensemble. This issue has been discussed dozens of times
across this list. Check the archives (and the literature) for details.
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.
See the manual, section 6.3, where this very topic is discussed.
-Justin
Thanks in advance.
Regards
Rama
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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