Re: inputPrefix merge error ABF

From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Mon Apr 01 2019 - 15:36:02 CDT

Are you sure that solvate_ua+ions.3.count is present in the NAMD
working directory? You should note that the position of the file given
in the Colvars configuration file is relative to the directory that
NAMD is called from, not the directory that the Colvars configuration
file is in.

Jeff
–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311
Website: http://jeffcomer.us

On Sun, Mar 31, 2019 at 11:48 PM Abhishek TYAGI <atyagiaa_at_connect.ust.hk> wrote:
>
> 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

This archive was generated by hypermail 2.1.6 : Mon Sep 16 2019 - 23:20:30 CDT