Re: [NAMD] Using ABF to study separation of two molecules

From: The Cromicus Productions (
Date: Mon Jan 23 2017 - 09:12:39 CST

Thanks Giacomo! About the biasing force, do I have to define it as an
external potential during the
Simulation or does defining the colvars and the method already take care of
sampling the range of
Possible values of the colvars I want?

On Monday, January 23, 2017, Giacomo Fiorin <>

> Hi Sebastian, ABF, metadynamics and umbrella sampling are all methods that
> allow you to compute one- and multi-dimensional PMFs. They rely on
> different free energy estimators (ABF measures the internal, or "system"
> forces acting on the variables, metadynamics targets a flat probability
> distribution so that the PMF is calculated directly from the biasing
> potential, umbrella sampling does the same but with a Gaussian distribution
> instead of a flat one).
> You can use any free energy estimator on an equilibrium MD simulation
> (internal forces or probability distribution), but you won't see much
> beyond the local minimum you're in. This is the reason why most free
> energy calculation methods use a biasing force or potential. The effects
> of this bias are automatically removed from the free energy estimate.
> To use methods based on collective variables, you need to decide which
> variables are accurate descriptors of your system. You may use similarity
> with a system previously published, but a general rule for the choice of
> collective variables simply does not exist.
> The choice of variable / reaction coordinate is much more important than
> the method you will use on it.
> Giacomo
> On Mon, Jan 23, 2017 at 2:00 AM, The Cromicus Productions <
> <javascript:_e(%7B%7D,'cvml','');>> wrote:
>> Hi everyone,
>> I'm new to free energy calculations using NAMD but currently I'm studying
>> how two molecules separate.
>> To do so, in simulations I untwist and separate them (under normal
>> conditions they separate in milliseconds).
>> If I want to obtain the free energy through the reaction coordinate,
>> which is the most convenient thing to use,
>> ABF, metadynamics, umbrella sampling?
>> Also, if I want to use for example ABF, do I need to run it during a
>> simulation where I do this mechanism or do
>> I just have to sample during equilibrium steps of the molecules? If I
>> sample during equilibrium for a few nanoseconds
>> It doesn't seem natural to be able to get to the barrier, but If I
>> simulate during my mechanism aren't I putting external
>> Forces that will modify the real free energy?
>> Thank you very much,
>> Sebastian
> --
> Giacomo Fiorin
> Associate Professor of Research
> Institute for Computational Molecular Science (ICMS)
> College of Science and Technology, Temple University
> 1925 North 12th Street (035-07), Room 704D
> Philadelphia, PA 19122-1801
> Phone: +1-215-204-4213
> Scholar:
> Personal:
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> *"As computer programmers we have a responsibility to make sure that we
> run the computers instead of the computers running us."* - Steve Oualline

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