Re: Specifying a pull direction with COLVARS

From: Jérôme Hénin (
Date: Tue May 26 2020 - 09:19:04 CDT

Hi Selemon,

I can't reproduce the error here. Can you send the log file from NAMD's standard output?

Another point: you don't need to set wall potentials on the angles if the ranged are 0,180 or -180,180, that is, the full range of the angles: the wall potentials won't do anything.

Finally, if you send the simplest example you have that fails, it will be easiest to understand where the error is.


----- On 26 Mai 20, at 6:52, Selemon Bekele wrote:

> Hi there,
> I am trying to run a pulling simulation using the COLVARS module in NAMD
> (version 2.13). This is my first time to use COLVARS and am still learning
> about it.
> The goal is to pull an ion from its binding pocket in a protein. I want to
> specify a pull direction by scanning the distances between the ion and the
> center of mass of the coordinating atoms, the polar angle (polarTheta) and the
> azimutal angle (polarPhi) in a coordinate system centered on the center of
> mass. I need the protein RMSD to be restrained.
> Simulations with a simple distance colvars run fine. However, when I try to
> include the angles, the simulation fails. I have attached the necessary files
> if anyone can spot what I am doing wrong. All files referenced in the input
> scripts have been used before and have no issues. May be the input structure is
> not compatible with the version of COLVARS in the NAMD version I am using. I
> am not sure why it works for a simple distance colvars though. A simulation
> with only polarPhi or polarTheta also fails with the same error message which
> is shown below.
> ==========
> TCL: parameter unknown for NAMD config parameter
> FATAL ERROR: parameter unknown for NAMD config parameter
> while executing
> "width"
> invoked from within
> "cv config "
> # This string is not Tcl code, but you can still use in here Tcl variables,
> # such as ${numsteps}, and bracket expansion, such as [output..."
> (file "drag_3d.namd" line 5)
> invoked from within
> "source drag_3d.namd "
> (file "smd_s0.namd" line 128)
> [0] Stack Traceback:
> [0:0] CmiAbortHelper+0x6b [0xdd761b]
> [0:1] _Z8NAMD_diePKc+0x70 [0x64ceb0]
> [0:2] _Z18after_backend_initiPPc+0x20e [0x65e0be]
> [0:3] main+0x36 [0x5e4596]
> [0:4] __libc_start_main+0xf5 [0x2b43821c83d5]
> [0:5] [0x5e76ac]
> ================
> I have searched the mailing list and the internet but have not found an answer
> to my satisfaction. I hope someone may have a clue.
> Thanks in advance,
> Selemon

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