Question about qdata.txt file and force matching

[Lee-Ping Wang]

That's strange - I would assume it's a problem with my script and not VMD, although I am using version 1.9.1 (the newest version). Does VMD print out any error messages when you load the files or attempt to change the frame number?

Thanks,

- Lee-Ping

[Noelia Beatriz Luque]

yes!
After loading the last force it says

can't set "vmd_frame(2)": invalid command name "min"

[Lee-Ping Wang]

Hi Noelia,

Hmm, it could be the VMD version. If you're not using version 1.9.1, can you update the version and retry?

I loaded the forces successfully from your attached file, and VMD gives me the following messages:

Code: Select all

leeping@sniffy:~/temp/drawforces$ vmd -e drawforces.vmd -args all.gro QMforce.xyz MMforce.xyz 
Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
Info) http://www.ks.uiuc.edu/Research/vmd/                         
Info) Email questions and bug reports to vmd@ks.uiuc.edu           
Info) Please include this reference in published work using VMD:   
Info)    Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual   
Info)    Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 8 CPUs detected.
Info) Free system memory: 3513MB (88%)
Warning) Detected a mismatch between CUDA runtime and GPU driver
Warning) Check to make sure that GPU drivers are up to date.
Info) No CUDA accelerator devices available.
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this optional X server feature.
Info) OpenGL renderer: Gallium 0.4 on llvmpipe (LLVM 0x300)
Info)   Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF) 
Info)   Full GLSL rendering mode is available.
Info)   Textures: 2-D (4096x4096), 3-D (512x512x512), Multitexture (8)
Info) Dynamically loaded 2 plugins in directory:
Info) /home/leeping/local/lib/vmd/plugins/LINUXAMD64/molfile
Lines
blue2 orange3 green red violet
#=================================================================================================#
#| Usage: Launch VMD with 'vmd -e drawforces.vmd -args coors.xyz forces1.xyz (forces2.xyz ... )' |#
#|        where EACH forces.xyz has the same number of atoms and frames as coors.xyz             |#
#|        Or, open VMD and run 'play coors.xyz forces1.xyz (forces2.xyz ... )'                   |#
#=================================================================================================#
all.gro
Info) Using plugin gro for structure file all.gro
Info) Using plugin gro for coordinates from file all.gro
Info) Determining bond structure from distance search ...
Info) Finished with coordinate file all.gro.
Info) Analyzing structure ...
Info)    Atoms: 16
Info)    Bonds: 10
Info)    Angles: 0  Dihedrals: 0  Impropers: 0  Cross-terms: 0
Info)    Bondtypes: 0  Angletypes: 0  Dihedraltypes: 0  Impropertypes: 0
Info)    Residues: 6
Info)    Waters: 0
Info)    Segments: 1
Info)    Fragments: 6   Protein: 0   Nucleic: 0
0
Loading forces from xyz file: QMforce.xyz
Info) Using plugin xyz for structure file QMforce.xyz
Info) Using plugin xyz for coordinates from file QMforce.xyz
Info) Determining bond structure from distance search ...
Info) Finished with coordinate file QMforce.xyz.
Info) Analyzing structure ...
Info)    Atoms: 16
Info)    Bonds: 0
Info)    Angles: 0  Dihedrals: 0  Impropers: 0  Cross-terms: 0
Info)    Bondtypes: 0  Angletypes: 0  Dihedraltypes: 0  Impropertypes: 0
Info)    Residues: 16
Info)    Waters: 0
Info)    Segments: 1
Info)    Fragments: 16   Protein: 0   Nucleic: 0
Loading forces from xyz file: MMforce.xyz
Info) Using plugin xyz for structure file MMforce.xyz
Info) Using plugin xyz for coordinates from file MMforce.xyz
Info) Determining bond structure from distance search ...
Info) Finished with coordinate file MMforce.xyz.
Info) Analyzing structure ...
Info)    Atoms: 16
Info)    Bonds: 0
Info)    Angles: 0  Dihedrals: 0  Impropers: 0  Cross-terms: 0
Info)    Bondtypes: 0  Angletypes: 0  Dihedraltypes: 0  Impropertypes: 0
Info)    Residues: 16
Info)    Waters: 0
Info)    Segments: 1
Info)    Fragments: 16   Protein: 0   Nucleic: 0
3
16
0
vmd > 

[Noelia Beatriz Luque]

I am using that version:

Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)

[Lee-Ping Wang]

Hmm, that's very weird .. Are you running on Windows or Mac OS? I'm running on Linux.

In any case, the command "min" only appears on line 82 in my script. Try commenting out that line. You will get oversized arrowheads for tiny arrows, but it might work.

[Lee-Ping Wang]

If you're not using Linux, one possibility is that different operating systems can use different characters to indicate the end of a line. Linux uses \n, whereas Mac OS uses \r and Windows uses \r\n. Can you open the script in a text editor, and look at the script with "cat", and let me know if anything seems out of the ordinary?

[Noelia Beatriz Luque]

# set radius [min [expr 0.1 * [veclength $vec]] $radius]

I am running it in linux and as you see there is nothing unusual.
I got huge arrows! (see the attach)

[Lee-Ping Wang]

Hahahaha, I laughed out loud from that picture.

There are two options for making this work:

On line 82, I have no idea why the "min" command doesn't work, but it's not important and you can try replacing it with this expression:

Code: Select all

    set radius [expr 0.1 * [veclength $vec]]

On line 122, the "constant" radius is set manually, and for some reason it's set to 1.2. I don't know where this number came from, but it results in enormous arrowheads. You can play with this number until the arrows look reasonable.

Code: Select all

            lappend frcgraphs [vmd_draw_vecfield $molid $frcdata 3.0 35 1.2]

[Noelia Beatriz Luque]

Thanks a lot!!!!!

both options worked well, but I think I prefer the first one!
I got bigger MM Forces than QM forces in one snapshot...
I have to check it out!
THANKS a lot!!!!
BR,
noelia

[Lee-Ping Wang]

No problem, I'm glad the script worked! Still, it's very weird that VMD would not recognize such a simple function as "min".

The bigger MM forces could be caused by using the LJ functional form, since it's too sharp in the repulsive region. You can try the Buckingham interaction as an alternative.

Thanks,

- Lee-Ping