From: Francesco Pietra (
Date: Sat May 30 2015 - 10:19:32 CDT


I could calculate the radius of gyration on my computer (VMD 1.9.1) with
short, test files, following command

vmd -e rgyr.tcl -dispdev none > rgyr_npt35.tx

The same tlc script failed to perform on a long file at the computing
center, following commands

module load profile/advanced vmd

vmd -e rgyr.tcl -dispdev none > rgyr_npt35.txt

The tlc script reads:

# calculates radius of gyration using bigdcd

# run with vmd in text mode

source bigdcd.tcl

proc gyration { frame } {
   global ref sel all outfile
   $all move [measure fit $ref $sel]
   puts "$frame: [measure rgyr $sel]"
   puts $outfile "[measure rgyr $sel]"
set mol [mol addfile XAN_O2-out_watbox_isotonic.pdb type pdb waitfor all]
set all [atomselect $mol all]
set ref [atomselect $mol "protein and backbone and noh" frame 0]
set sel [atomselect $mol "protein and backbone and noh"]
set outfile [open gyration.dat w]
bigdcd gyration dcd npt-35.dcd
close $outfile

Permission for the tcl script


I also tried by giving execute permission, although it should be unnecessary


The wrong rgyr_npt35.txt from the computing center reads:

Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
Info) Email questions and bug reports to
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, 16 CPUs detected.
Info) Free system memory: 115938MB (90%)
Info) Creating CUDA device pool and initializing hardware...
Info) Detected 2 available CUDA accelerators:
Info) [0] Tesla K40m 15 SM_3.5 @ 0.75 GHz, 11GB RAM, KTO, AE2, ZCP
Info) [1] Tesla K40m 15 SM_3.5 @ 0.75 GHz, 11GB RAM, KTO, AE2, ZCP
Info) Detected 2 available TachyonL/OptiX ray tracing accelerators
Info) Dynamically loaded 2 plugins in directory:
Info) /cineca/prod/tools/vmd/1.9.2/binary/lib/vmd/plugins/LINUXAMD64/molfile
too many nested evaluations (infinite loop?)
Info) Using plugin pdb for structure file XAN_O2-out_watbox_isotonic.pdb
Info) Using plugin pdb for coordinates from file
Info) Determining bond structure from distance search ...
Info) Finished with coordinate file UOX_XAN_O2-out_watbox_isotonic.pdb.
Info) Analyzing structure ...
Info) Atoms: 187233
Info) Bonds: 131246
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 57547
Info) Waters: 56031
Info) Segments: 37
Info) Fragments: 56371 Protein: 4 Nucleic: 0
invalid command name "bigdcd"
invalid command name "bigdcd_wait"
vmd > Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
Info) Exiting normally.

I wonder whether
means that the plugins are not loaded.

The same failure was met with related tcl scripts for calculationg the
center of mass and the rmsd, both running correctly on my computer.

Thanks for advice
francesco pietra