From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri May 29 2015 - 12:30:43 CDT

Josh and Bennio, thanks a lot. It works now (also gyration, where I had the
same mistake)
francesco

On Fri, May 29, 2015 at 5:58 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> set $mol [mol new blg.psf type psf waitfor all]
>
> should be
>
> set mol [mol new blg.psf type psf waitfor all]
>
> -Josh Vermaas
>
>
> On 05/29/2015 09:35 AM, Francesco Pietra wrote:
>
> Hello
>
> What is wrong in my centermass.tcl script below? (taken from the web)
>
>
>
> # This computes the center of mass for each frame in the DCD file.
> #
> source bigdcd.tcl
>
> proc mycenter { frame } {
> global all
> puts "$frame: [measure center $all weight mass]"
> }
> set $mol [mol new blg.psf type psf waitfor all]
> set all [atomselect $mol all]
> $all global
> bigdcd mycenter auto blg.dcd
> quit
>
>
>
> as command
>
>
> vmd -e centermass.tcl -dispdev none > centermass.out
>
>
> reports:
>
> Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_Research_vmd_&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=mFdAd78H9E0voZDT-ASzdXF0qpPiRvPxtRk2x5efirA&s=G1xth-FBkImB5eAjB_6dWq-lHwpbi4z0V2-3Mv59LFI&e=>
>
> Info) Email questions and bug reports to vmd_at_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, 4 CPUs detected.
> Info) Free system memory: 7209MB (90%)
> 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
> can't read "mol": no such variable
> can't read "mol": no such variable
> can't read "all": no such variable
> molinfo: get: no molecule exists with id -1
> Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
> Info) Exiting normally.
> vmd >
>
>
>
> Is blg.pdb lacking? These blg files work finely with the related rmsd
> script from the same source.
>
> Thanks
>
> francesco pietra
>
>
>
>