Re: ABF inFiles

From: Jerome Henin (
Date: Thu Jun 21 2007 - 11:57:35 CDT

Hi Vaithee,
Your first reaction is correct: since data read through niFiles gets included
in the output file, in most cases one should only include the output from the
previous run. We made it possible to read several files there only to make it
easier for users to switch between several smaller "windows" and larger ones,
merging the results of several previous runs.
In addition to checking the number of samples in each bin, you can look in the
output for this message:
TCL: ABF> Loading previous force data from meoh01.dat ...
TCL: ABF> 2454014 sampling points retrieved
The number of samples there may be a bit smaller than the number of timesteps
if the system has spent some time at the boundaries, where no samples are

You are not the only person to have been confused about this, so I will think
of updating the manual to make this point clearer.


On Thursday 21 June 2007 12:03, Subramanian Vaitheeswaran wrote:
> I have a question about combining the ABF output from multiple data sets
> using the inFiles entry in the configuration file.
> SET2 reads restart files from SET1 and ABF section of the configuration
> file I have the following entry: abf inFiles {../SET1/abf.pmf}
> So, SET2 will include data from SET1 in calculating the PMF.
> SET3 then reads restart files from SET2. To combine the data from all
> three sets, should the configuration file read: (1) abf inFiles
> {../SET2/abf.pmf} or,
> (2) abf inFiles {../SET1/abf.pmf ../SET2/abf.pmf} ?
> I thought SET2/abf.pmf would include data from SET1, so it should be (1),
> but looking at the number of samples in each bin, I am not sure any more.
> Any help is much appreciated.
> thanks,
> Vaithee

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