inputPrefix merge error ABF

From: Abhishek TYAGI (
Date: Sun Mar 31 2019 - 23:46:47 CDT

Dear Experts,

After finishing ABF calculations, I need to combine them for post-processing of data. I have used inputPrefix to combine the files, but I have faced error as shown below. (I am using NAMD_2.13)

The keyword were set in the colver input file:

abf {
   colvars NormalMolMem
   fullSamples 500
   historyFreq 20000
   updateBias no
   inputPrefix solvate_ua+ions.3 solvate_ua+ions.4 solvate_ua+ions.5 solvate_ua+ions.6 solvate_ua+ions.7

Error in log file as follows:

colvars: Collective variables initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "abf" instance.
colvars: # name = "abf1" [default]
colvars: # colvars = { NormalMolMem }
colvars: # outputEnergy = off [default]
colvars: # timeStepFactor = 1 [default]
colvars: # applyBias = on [default]
colvars: # updateBias = off
colvars: WARNING: ABF biases will *not* be updated!
colvars: # hideJacobian = off [default]
colvars: Jacobian (geometric) forces will be included in reported free energy gradients.
colvars: # fullSamples = 500
colvars: # inputPrefix = { solvate_ua+ions.3, solvate_ua+ions.4, solvate_ua+ions.5, solvate_ua+ions.6, solvate_ua+ions.7 }
colvars: # outputFreq = 20000 [default]
colvars: # historyFreq = 20000
colvars: # shared = off [default]
colvars: # maxForce = [default]
colvars: # integrate = on [default]
colvars: Reading sample count from solvate_ua+ions.3.count and gradient from solvate_ua+ions.3.grad
colvars: Error opening ABF samples file solvate_ua+ions.3.count for reading
FATAL ERROR: Error in the collective variables module: No such file or directory

The colvarsConfig file is placed in the same folder with the other files, still can't find the files, though the files are next to the input files, I am sure the path is correct.

Please suggest what can be done in this situation.

Thanks in advance for your time


Abhishek Tyagi, PhD
Research Associate
Chemical and Biological Engineering
Hong Kong University of Science and Technology
Clear Water Bay, Hong Kong

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