[gmx-users] trouble using tables with 5.1

XAvier Periole X.Periole at rug.nl
Mon Jul 18 13:49:52 CEST 2016


Dears,
Note: At the end of the message I provide a solution found while writing the email ...

I am having troubles feeding mdrun my tabulated bonded terms through tables. The manual does not indicate any change in that respect … 

I used to run this with gmx-463 with the command looking like:
mdrun <options> -tableb /path/table 

my tabulated potentials being named:
table_a0.xvg table_a1.xvg 
table_d0.xvg … table_d13.xvg 

With the same syntax (-tableb table) using gmx5.1 I get the following error message:
-----
Error in user input:
Invalid common-line options 
  In command-line option -tableb
    File ‘table’ does not exist or is not accessible.
    The following extensions were tried to complete the file name

if I add .xvg to the name table (-tableb table.xvg) I get the error:
----
Error in user input:
Invalid common-line options 
  In command-line option -tableb
    File ‘table’ does not exist or is not accessible.

if I give the fill name of one table (-table table_a0.xvg) I get the error:
——
System I/O error:
Library file ‘table_a0_a0.xvg’ not found in the current directory no in the default directories.
The following path …

Solution: then is I give the name table.xvg (-tableb table.xvg) and create an empty file then it all goes smooth and the files are red and mdrun … 

Beautiful, but might be some funky stuff happening that could be fixed. 

Tks,
XAvier.


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