solved inputPrefix for ABF

From: Branko (
Date: Sun Oct 21 2012 - 15:24:43 CDT

Hi Giacomo,

Thanks a lot, your advices solve the problem. I have a merged file
(output files (count and grad) are 'biger' than initial one and the PMF
likes as superimposition of the PMFs of all three runs). If possible,
please add to NAMD u.g that list of strings should be as: the name of
files one AFTER other; not one below the other (end of lines likely is
not a problem, I switched between the dos and unix endlines and both
works). Also if I add the common part of the name of count and grad
files from previous simulations (I understand in this way 'prefix'),
program did not recognized my input, i.e. full names of files (without
'extensions' i.e. .grad and .count) should be provided - maybe this
could be changed in some of next releases.



On 10/21/2012 8:43 PM, Giacomo Fiorin wrote:
> Hello Branko, the inputPrefix keyword must be within the abf {...}
> block. It will be recognized there.
> If there is any other issue in opening the files when you do that, it
> may be Windows-related and we'd like to know if any error happens
> because of that. Most likely it should work though.
> Bests
> Giacomo
> On Sat, Oct 20, 2012 at 5:36 PM, Branko <
> <>> wrote:
> Jerome, Giacomo,
> I performed ABF calculations in the three windows 10+10+10 ns, in
> each calculation program terminated regularly and produces .count,
> .grad and .colvars.state files. Then I try to 'merge' all three
> ABF outputs using 'inputPrefix' keyword. Unfortunately
> unsuccessfully. First I try to add this keyword in the basic NAMD
> configuration file under "Other Parameters':
> # Other parameters
> colvars on
> colvarsConfig adicioni
> inputPrefix name_of_the_file(s) (without extensions i.e. grad,
> count, colvars,state)
> but program terminated with message that 'inputPrefix' is not
> recognized in this context
> Them I moved this keyword to colvars configuration file, below
> colvarsTrajFrequency 1
> colvarsRestartFrequency 1000
> analysis on
> _inputPrefix name_of_the_file(s)_
> all other colvar parameters exist in this file, and were the same
> as for three calculations
> Program then terminated after initiation of the Collective
> variables with message 'Error: keyword "inputprefix" is not
> supported, or not recognized in this context'
> Please let me know where I should put this keyword and how
> (exactly) list of strings should looks, if I have three ABF
> outputs with names:
> abfoutput_1, abfoutput_2, abfoutput_3
> I try to perform all described in NAMD2.9 for Windows, while
> calculations were performed on Linux ibverbs version.
> Thanks a lot
> Branko

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