Re: inputPrefix for ABF

From: Giacomo Fiorin (
Date: Sun Oct 21 2012 - 13:43:52 CDT

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.


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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