On Wed, 29 Apr 2015 00:44:57 -0400
Laura Tociu <ltociu.princeton.edu> wrote:
> Another thing that I've been meaning to ask for a long time but is a
> little unrelated is how important is it to do MMPBSA on an
> equilibrated segment of a trajectory, and is RMS enough to establish
> if this equilibration has been achieved? I am a little confused
> because theoretically in order for an MMPBSA+ entropy calculation to
> give ensemble-average type quantities the trajectory should be
> equilibrated and long I believe. This should be especially true for a
> quasi-harmonic approximation since the assumption is that the system
> lies in what can be approximated as a broad energy well (i.e.
> equilibration I assume). Nonetheless in many articles I see people
> running simulations for a certain time and then performing mmpbsa on
> the last few ns of the trajectories, without any reference to whether
> equilibration was achieved or not. I'd be very thankful if someone
> could shine light on this matter for me.
What does "equilibrium" really mean in this context? Thermodynamic
equilibrium probably rather not. I think this is a term that is often
used fast and loose. Typically, it means something like "I looked at
this property and it showed the asymptotic behaviour I expected to see
so I call the system equilibrated". To be fair, the amount of time one
can put into a project is limited.
QHA measures collective global motions which are notoriously slow to
converge.
Cheers,
Hannes.
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Received on Thu Apr 30 2015 - 03:30:03 PDT
