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

[Justin A. Lemkul]

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
> 
> 

-- 
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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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