RE: ABF question (sampling and colvars output file)

From: Parisa Akhski (
Date: Mon Feb 07 2011 - 14:27:03 CST

Hi Jerome,

That will make everything much easier. Thanks a lot and I will be waiting for it.



-----Original Message-----
From: on behalf of Jérôme Hénin
Sent: Mon 2/7/2011 12:16 PM
To: Parisa Akhski
Subject: Re: namd-l: ABF question (sampling and colvars output file)
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.
>> This is really necessary for my system.
>> Many thanks,
>> Parisa

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