VMD-Tools

VMD Tools (2015.12.31)

-Functions-

A. chview: Change Viewpoint by Moving Atomic Configurations
B. topdb: Export Selected Frames and Atoms as PDB a Trajectory File
C. pickconfig: Export Selected Frames as a Scaled Coordination File
D. ssr: Render Snapshots of Selected Frames
E. makebonds: Make Bondlists for All Frames
F. readbonds: Read Bondlist and Update Every Frames
G. readdata: Read Trajectory Value as "User" Variable

Setup

1. Select "VMD Main -> Extansions -> TkConsole"

2. Execute "source (path)/misawa.tcl"

3. Execute functions

A. chview: Change Viewpoint by Moving Atomic Configurations

(How to use)

chview -shift { $x $y $z }:
--- shift atomic positions in {$x $y $z} (ang.) in boundary box.
|$x|, |$y| and |$z| must be smaller than Lx, Ly and Lz

chview -com "$selection":
--- fit center of mass of $selection to center of view

chview -gc "$selection":
--- fit geometrical center of $selection to center of view

chview -reset
--- reset view

Example: chview -com "name O H"
--- fit center of mass of oxygen and hydrogen to center of view

Memo: Input lattice constant is required
("pbc set {$a $b $c $alpha $beta $gamma} -all" on Tk Console)
Only for orthorhombic cell

B. topdb: Export Selected Frames and Atoms as a PDB Trajectory File

(How to use)

topdb $i $j $filename
$i: start frame
$j: end frame

topdb -skip $sk -sel $selection $i $j $filename
$selsction: selection of atoms (like as "name Fe O")
$sk: skip frames

Example: topdb -skip 5 0 100 trajectory.pdb

C. pickconfig: Export Selected Frame as a Scaled Coordination File

(How to use)
pickconfig $frame $filename
$frame: default frame is "now"
$filename: default filename is "Config.dat"

Memo: Input lattice constant is required
("pbc set {$a $b $c $alpha $beta $gamma} -all" on Tk Console)
Only for orthorhombic cell

D. ssr: Render Snapshots of Selected Frames

(How to use)

ssr -frames $i $j
$i: initial frame number
$j: final frame number

ssr -frame $i
$i: render frame

(other options)
ssr -frame $i -form $text -skip $s -rend $r
$text: format type (default: tga)
$s: skip every $s frame (default: 1)
$rend: render type (default: 0)
$r = 0: Snapshots
$r = 1: Internal Tachyon

Example: ssr -frames 0 100 -rend TachyonInternal
--- Frame000.tga ~ Frame100.tga will be created by Tachyon

E. makebonds: Make Bondlists for All Frames

(How to use)

makebonds $filename
(default filename is "./bondlist.dat")
then enter the cutoff distances in ang.

makebonds -pbc $filename
--- make bondlist with considering PBC
(please execute "readbonds" with "-pbc" option
when you apply a bondlist created with this option)

note: cutoff distance should be less than 3.0 ang.

bondlist format:

3 5 10 neighbors of atom 1, step 0
neighbors of atom 2, step 0 (if no neighbors: empty)
1 12 100 neighbors of atom 3, step 0
.
.
.
30 40 50 neighbors of atom n, step 0
3 5 10 12 neighbors of atom 1, step 1
3 neighbors of atom 1, step 1
.
.
.

Memo: Input lattice constant is required
("pbc set {$a $b $c $alpha $beta $gamma} -all" on Tk Console)
Only for orthorhombic cell
VMD will be stop if there are too many atoms or frames
Create bondlists on other workspace (not on VMD) is recommended

F. readbonds: Read Bondlist and Update Every Frames

(How to use)

readbonds $filename
default filename is "./bondlist.dat"

readbonds -pbc $filename
--- remove PBC bond with keeping "numbonds"
if bond distance > 3 ang., it will be considered as PBC bond

Bondlist is available only for "Bonds" or "CPK" in Representation.

The bondlist is available only for current box.
(if "pbc wrap -shiftcenter" or "chview" is done after readbonds,
"Bonds" or "CPK" will not represent exactlly.)

bondlist format:

3 5 10 neighbors of atom 1, step 0
neighbors of atom 2, step 0 (if no neighbors: empty)
1 12 100 neighbors of atom 3, step 0
.
.
.
30 40 50 neighbors of atom n, step 0
3 5 10 12 neighbors of atom 1, step 1
3 neighbors of atom 1, step 1
.
.
.

Memo: Input lattice constant is required
("pbc set {$a $b $c $alpha $beta $gamma} -all" on Tk Console)
Only for orthorhombic cell

G. readdata: Read Trajectory Value as "User" Variable

(How to use)

readdata $filename -str $i $j -var $var
$filename: path of datafile
$i, $j: data strength (default: $i = 4, $j = 6)
$var: variable name (default: user) e.g. user, user2, user3, ...

example:
readdata ./coordination.dat -var use2

datafile format:

DATA 1.0 value for atom 1, step 0
DATA 2.0 value for atom 2, step 0
DATA 1.5 value for atom 3, step 0
.
.
.
DATA 1.2 value for atom n, step 0
END
DATA 1.0 value for atom 1, step 1
DATA 2.0 value for atom 2, step 1
.
.
.