Re: Is two colvars file output possible during single simulation (ABF/2.7b)

From: Giacomo Fiorin (
Date: Sun Feb 21 2010 - 00:15:53 CST

OK, then you can slice the 2-D pmf that you obtain from abf_integrate at a
certain value of the second colvar (r. gyr.), or even better, integrate over
it for every point of the first colvar (distance). Integrate means that you
take the free energy as a function of the distance and of the r. gyr., you
average over all points with the same value of the distance using the
Boltzmann weight. abf_integrate doesn't do that, but the .pmf file is
simple to read, it's very easy to do this with a small script.


---- ----
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
---- ----

On Sat, Feb 20, 2010 at 6:58 AM, Branko <> 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
> surface".
> 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. :-) .
> Sincerely
> Branko
> Giacomo Fiorin wrote:
> Hi Branko, I failed to parse the following: "the (for example) both needed
> (defined)".
> 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
> ---- ----
> 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:
> ---- ----
> On Fri, Feb 19, 2010 at 8:51 AM, Branko <><>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.
>> Sincerely
>> Branko
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