Various practical colvar module related questions

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue Jan 18 2011 - 11:31:46 CST

Dear all (especially Jrme:),

I am about to start some more extensive ABF/metadynamics calculations, but I
have some practical problems/questions:

*1) How to choose the values for the constants such as (LangevinDamping,
fullSamples, width of colvar, lowerWallConstant, upperWallConstant)?*
Chipot and Henin,2005 <http://dx.doi.org/10.1063/1.2138694> have tested the
effect of these parameters by comparing them to a longer reference
unconstrained MD simulation. All the parameters can significantly effect
the calculated FES. But I find it hard to choose the rigth values without a
reference MD run.
And overdameped system does not diffuse efficiently, large or small
WallConstatns can affect the potential at the borders, and the fullSamples
seems to affect the standard error. In Fig 3c why is the error so large? I
would think that the more samples one has the better the estimate of the
average force.

I'll be working in water and membrane (probably using projections along a
vector as colvars), so I'm thinking of:
rigidbonds all
timestep 2 ps
nonbondedFreq 1
fullElectFrequency 2
langevinDamping 1 1/ps
fullSamples 500???
width 0.4 A
lowerWallConstant 5???

How can one be sure the choice of the parameters is correct? Is it better to
have smaller bins and less fullSamples or more fullSamples and larger bins?

*2) Must ABF simulations be preformed in a NVT ensembe? What about
metdynamics?*
The free energy is the sensible measure in a NVT ensemble. What happens if
one runs ABF simulations at NPT? (I suppose it would be to naive to expect
that one obtains the free enthalpy:). But in liquid systems the pV term is
small, so does this even matter?

*3)How does one know when/if an ABF simulation has converged?*
This one is probably easy, I would imagine when the histogram of the colvars
becomes flat (at least in the region of interest)? Does the same hold for
metadynamics? Or perhaps it's enough just to see if the FES does not change
any more (like it says in the ABF tutorial)

*4)Can a metadynamics simulation also be split in to smaller regions
(windows)?*
Is it feasible to split the FES into smaller regions? When using multiple
walkers the simulations get slower and slower (because one cannot use
grids).

*5)How does one obtain the probability density from the free energy profile?
*
In a NVT ensemble the probabilty of a state with energy Ej is given by the
Boltzmann distribution.

Pj=exp(-beta*Ej)/sum_over_j(exp(-beta*Ej)).

But equation (3) in Henin and
Chipot,2004<http://dx.doi.org/10.1063/1.1773132> seems
to imply I'm missing something:

A(x)=-1/beta*ln(P(x)) + A0 ==> P(x) =exp(-beta*Ej)/exp(A0)

Since A = E - TS, would this imply that the TS term is considered constant
along x? (and is this valid? I don't think so...)

Thank you very much for your time and help,
best regards,
Ajasja Ljubeti,
Young researcher,
Department of solid state physics (F5),
Institute Joef tefan,
Ljubljana, Slovenia

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