From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Feb 24 2010 - 11:55:26 CST
To extract a "marginal" (one-dimension) PMF, you should:
1) compute the 2d probability distribution from the PMF (p(xi) = exp(-A(xi)/RT))
2) sum over one of the dimensions to get a 1d distribution
3) calculate the inverse of step 1) to get the 1d PMF
On 20 February 2010 06:58, Branko <bdrakuli_at_chem.bg.ac.yu> wrote:
> Hi Giacomo,
> First sorry for unclear question. I use two colvars to obtain "free energy
> surface" (PMF), but my unclear question was could I obtain "one dimensional
> PMF" for the one of two colvars used for calculation of "free energy
> Briefly, one of colvars is distance between the certain atom groups, the
> other is radius of gyration of some other atoms. After the finishing of MD
> simulation I have count and grad files, which I subsequently processed with
> abf integrate,than obtain <file>.grad.pmf and make the plot with GNU plot.
> So question was, can I obtain simultaneously (in same MD run) also PMF
> output only for distance (colvar).
> But your answer is very clear. Also I am strongly decide to use ABF in
> subsequent calculations, at least for outgoing project. :-) .
> Giacomo Fiorin wrote:
> Hi Branko, I failed to parse the following: "the (for example) both needed
> What do you also mean by "colvars output"?
> If you mean output the values of multiple variables, sure, it's always
> possible to output the values and other parameters of colvars not involved
> in ABF or other methods.
> If you mean having two PMFs for the price of one, please do keep in mind
> that running a ABF calculation during the same MD simulation as another ABF
> simulation won't work. Once the system is driven out of equilibrium by one
> instance of ABF, the other one will measure incorrect forces. Before you
> ask, this holds for every free energy calculation method that's not straight
> equilibrium MD.
> ---- ----
> Giacomo Fiorin
> ICMS - Institute for Computational Molecular Science
> Temple University
> 1900 N 12 th Street, Philadelphia, PA 19122
> work phone: (+1)-215-204-4216
> mobile: (+1)-267-324-7676
> mail: giacomo.fiorin_at_gmail.com
> ---- ----
> On Fri, Feb 19, 2010 at 8:51 AM, Branko <bdrakuli_at_chem.bg.ac.yu> wrote:
>> Hi Jerome,
>> Please let me know is possible to obtain two colvars output: one for the
>> single collective variable, and the other for the (for example) both needed
>> (defined). It is "economic" to collect data in this way for the longer
>> simulations. If possible, are two colvar inpput definition files should be
>> defined or this could be solved in some other way. Thank a lot.
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