From: KK R (
Date: Fri Jul 10 2015 - 14:51:23 CDT

Dear VMD users,
I am trying to use bigdcd for wrapping, unwrapping and writeing dcd file
using VMD text mode with the command:

vmd -dispdev text -e Script.tcl

Script.tcl is:

source bigdcd.tcl
package require pbctools
proc nwc { frame } {
global sel nf
for { set i 1 } { $i < $nf } { incr 1 } {
$sel frame $i
$sel [pbc unwrap -first 0] waitfor all
$sel [pbc wrap -centersel "protein" -center com -compound residue -all]
waitfor all
$sel [animate write dcd Wrappeddcd.dcd] waitfor all
mol load psf Mypsf.psf
set sel [atomselect top all]
set nf [molinfo top get numframes]
bigdcd nwc Mydcd.dcd

Running this script in VMD text mode

Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
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, 24 CPUs detected.
Info) Free system memory: 28821MB (89%)
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.
Info) Dynamically loaded 2 plugins in directory:
Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile

psfplugin) Detected a Charmm31 PSF file
psfplugin) Detected a Charmm31 PSF EXTEnded file
Info) Using plugin psf for structure file ../Mypsf.psf
Info) Analyzing structure ...
Info) Atoms: 104687
Info) Bonds: 104375
Info) Angles: 94547 Dihedrals: 101453 Impropers: 1401 Cross-terms: 346
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 22866
Info) Waters: 22140
Info) Segments: 6
Info) Fragments: 22520 Protein: 1 Nucleic: 0
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
Info) Using plugin dcd for coordinates from file Mydcd.dcd
vmd >

I am not able to grab loophole(s) in my tcl script. Any suggestion would be

Thanks in advance!