Re: ABF question (sampling and colvars output file)

From: Jérôme Hénin (
Date: Mon Feb 07 2011 - 11:16:28 CST

Hi Parisa,

The code needed to write ABF "history files" is ready. It should be pushed
into the public CVS soon (and available in nightly builds).


On 7 February 2011 11:20, Jérôme Hénin <> wrote:

> Hi Parisa,
> There is unfortunately not much I can say that hasn't been said before. The
> most likely explanation is that some slow degrees of freedom that couple to
> your RC are drifting (or have drifted at some point in the simulation). In
> other words, maybe the RC is "not good enough" on this timescale. Maybe it
> is not "local" enough: ideally the reference group used to measure the ion's
> position should not move much with respect to the channel's walls. If the
> channel has some flexibility, this can be a problem. Maybe you could use
> residues that are closer to the pore, or even pore-lining, as reference
> group.
> One robust, but demanding criterion for convergence is that every region of
> the RC range has been visited several times, and that the PMF has not
> changed.
> So far there is no PMF history file option, but I will think of
> reintroducing it. To many users it is not necessary because long simulations
> are often split into short ones to facilitate job management on clusters and
> supercomputers. Also, the history can be reconstructed if the system forces
> are written to the colvars trajectory file - I understand this is not the
> most convenient way.
> Cheers,
> Jerome
> On 6 February 2011 22:20, Parisa Akhski <>wrote:
>> Dear NAMD experts,
>> I am performing ABF calculations to capture the ion movement along a
>> channel.
>> I have improved the sampling in some of the windows by dividing the whole
>> RC to several windows, however, there is still a big difference in the
>> number of samples at two ends of the window in some cases even after a long
>> simulation time (20 ns). I am wondering what may cause this and is there any
>> other solution to improve and smoothen sampling? I know increasing the
>> current number of windows may help, but any thing else I can try? The
>> position of the ion is already within the each window.
>> I have always seen people discuss this issue in the mailing list. I am
>> wondering if there is any criteria to estimate the quality of the sampling?
>> How do I know my sampling is good? If there is a huge difference in the
>> number of samples in different areas (between 10k to 150k) or even more in
>> one window but the force has converged (the pmf profile is not changing
>> anymore), are the results acceptable?
>> Also, in NAMD 2.6 the history file of the system is reported and there is
>> always access to the force and free energy (PMF profile) of the system at
>> different time steps for different bins, however, in NAMD 2.7 (colvars),
>> only the final information of force and free energy is reported in .pmf file
>> unless you just copy your data manually during the simulation. I am
>> wondering if there is any way to have these data at different time steps--0016367fb41555afa0049bb46542--

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