Colvars module error in loading atomic coordinates from a file.

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1

Hi all,

I am using the user-colvars package for my input script(attached). My input script includes this command:
fix restraint all colvars step4.0_minimization.col output colvarsoutput.txt

I have attached the step4.0_minimization.col my config file for the colvars module. Now as my colvars config file defines from the command: refPositionsFile restraints/bb_rmsd.ref; I have to load the atomic coordinates from this bb_rmsd.ref file. For this step lammps is giving me this error:
(copied the whole colvars screen output)

colvars: Reading new configuration from file "restraints/step4.0_minimization.col":
colvars: # indexFile = "colvar.index"
colvars: The following index groups were read from the index file "colvar.index":
colvars: bb_rmsd (1479 atoms).
colvars: sc_rmsd (1472 atoms).
colvars: # smp = on [default]
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 100
colvars: # colvarsRestartFrequency = 100
colvars: # colvarsTrajAppend = off [default]
colvars: # scriptedColvarForces = off [default]
colvars: # scriptingAfterBiases = on [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = "bb_rmsd"
colvars: Initializing a new "rmsd" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # scalable = on [default]
colvars: Initializing atom group "atoms".
colvars: # indexGroup = "bb_rmsd"
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Atom group "atoms" defined, 1479 atoms initialized: total mass = 1479, total charge = 0.
colvars: # refPositions = [default]
colvars: # refPositionsFile = "restraints/bb_rmsd.ref"
colvars: # refPositionsCol = "" [default]
colvars: Error: loading atomic coordinates from a file is currently not implemented.
ERROR on proc 0: Fatal error in the collective variables module.
(../colvarproxy_lammps.cpp:315)

step4.0_minimization.inp (1.47 KB)

step4.0_minimization.col (559 Bytes)

2

Hi all,

I am using the user-colvars package for my input script(attached). My
input script includes this command:
fix restraint all colvars step4.0_minimization.col output colvarsoutput.txt

I have attached the step4.0_minimization.col my config file for the
colvars module. Now as my colvars config file defines from the command:
refPositionsFile restraints/bb_rmsd.ref; I have to load the atomic
coordinates from this bb_rmsd.ref file. For this step lammps is giving me
this error:
(copied the whole colvars screen output)

​[...]​

colvars: Error: loading atomic coordinates from a file is currently not
implemented.
ERROR on proc 0: Fatal error in the collective variables module.
(../colvarproxy_lammps.cpp:315)

---------------------------

Now I am not able to understand whether I need to make any changes in the
colvars module because it says that this thing is currently not implemented
or I have made some other mistake somewhere. I have to run a simulation for
a kinase for which I have generated all these lammps input files from
Charmm-gui online tool. So, I think these files should be correct only.

​not implemented means, that you are trying to use a colvars feature, that
is currently​ not available with LAMMPS, as the corresponding functionality
has not been programmed. this will require some significant C++ programming
before it can be used. you either have to find an alternative or use a
different MD code, e.g. NAMD, where this feature is available.

axel.

3

Hi all, the Colvars module does have an XYZ file reader for this purpose. Try converting the file to XYZ format and make sure it has the .xyz extension.

Also, if your input comes from CHARMM-GUI developers, let them know that they should read the doc before implementing it. This is an error that is caused entirely by CHARMM-GUI.

Giacomo