From: Branko (bdrakuli_at_chem.bg.ac.yu)
Date: Sat Feb 20 2010 - 08:58:04 CST
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: giacomo.fiorin_at_gmail.com <mailto: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.
>
> Sincerely
>
> Branko
>
>
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