VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Thu Feb 10 2005 - 07:44:33 CST

>>> "LC" == Leyla Celik <lc_at_chem.au.dk> writes:

LC> Hi,

hi leyla,

LC> Is it possible to use the TkConsole to measure distances and angles in VMD? I
LC> have quite a lot of them, and it gets rather trivial to use the "Graphics -
LC> Labels" each time, especially when it is the same distances for different
LC> trajectories.

yes, have a look at the description of the 'label' command.

here is an example to write a 'trajectory' of the umbrella
motion of an ammonia molecule (by measuring the out-of-plane angle):

mol new {TRAJEC.xyz} type xyz waitfor all
label add Dihedrals 0/0 0/3 0/1 0/2

set fp [open "umbrella.dat" w]
set ts 0
set tsconv [expr 3.0 * 10.0 * 0.0241888428]
foreach dihed [label graph Dihedrals 0] {
    incr ts
    puts $fp [format "%12.5f %12.5f" [expr $ts * $tsconv] $dihed ]
}
close $fp

LC> By the way, does anybody know how many frames VMD can read from one dcd-file? It
LC> kind of crashed with 10000 frames.

this should be only limited by the amount of memory you have.

regards,
        axel.

LC> Thanks
LC> Leyla

LC> --
LC> Leyla Celik
LC> Ph.d. student
LC> Department of Chemistry
LC> University of Aarhus
LC> Langelandsgade 140
LC> DK-8000 Aarhus C
LC> Denmark
LC> Tel: +45 8942 3869
LC> e-mail: lc_at_chem.au.dk 

--
=======================================================================
Axel Kohlmeyer       e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.