From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Jan 23 2017 - 09:15:16 CST
You don't need to define manually the biasing force (ABF) or potential
(metadynamics / umbrella sampling), as they are defined by the methods.
You do need to define the range of values, though, in terms of lower and
upper boundary of a grid and bin width (metadynamics, ABF) or setting
multiple umbrella sampling windows.
This is the point where you check the doc to see how this is done:
http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html
https://github.com/colvars/colvars
Giacomo
On Mon, Jan 23, 2017 at 10:12 AM, The Cromicus Productions <
thecromicusproductions_at_gmail.com> wrote:
> 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 <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> 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 <
>> thecromicusproductions_at_gmail.com> 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 <(215)%20204-4213>
>>
>> Scholar: http://goo.gl/Q3TBQU
>> Personal: http://giacomofiorin.github.io/
>> Lab page: https://icms.cst.temple.edu/members.html
>>
>> *"As computer programmers we have a responsibility to make sure that we
>> run the computers instead of the computers running us."* - Steve
>> Oualline
>>
>>
>>
-- 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: http://goo.gl/Q3TBQU Personal: http://giacomofiorin.github.io/ Lab page: https://icms.cst.temple.edu/members.html *"As computer programmers we have a responsibility to make sure that we run the computers instead of the computers running us."* - Steve Oualline
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:21:01 CST