VMD script

# multiple folders or files
lsort -dictionary -increasing [glob phi*]

# load multiple files
foreach file [lsort [glob *.pdb]] {
mol addfile $file
}


Tcl tutorials
http://phaseit.net/claird/comp.lang.tcl/tcl_tutorials.html

VMD vmdrc options

############################################################################
# DESCRIPTION:
#
# VMD startup script. The commands here are executed as soon as VMD starts up
############################################################################


############################################################################
# Display Preferences
############################################################################

# menu
menu main move 525 30
menu main on

# animate
animate style once; # once/rock/loop

# display
display projection Orthographic; # Orthographic/Perspective
display nearclip set 0.01

# color
color Display Background 16; # 6/8/16 for silver/white/black
color Labels Bonds 0; # 0 for blue
color Labels Angles 1; # 1 for red

# axes
axes location lowerleft
axes location off

# stage
stage location off

# light
light 0 on

# rock
rock y by 1; # start the scene a-rockin'

# mouse
mouse rocking off


############################################################################
# Redefine Colors
############################################################################

color Name C 7; # 7 for green
color Type C 7

color Name F 12; # 12 for lime
color Type F 12


############################################################################
# New Material
############################################################################

# Glass: a very transparent Material
material add Glass
material change ambient Glass 0.00
material change specular Glass 0.50
material change diffuse Glass 0.65
material change shininess Glass 0.53
material change opacity Glass 0.15

# SemiTrans
material add SemiTrans
material change ambient SemiTrans 0.00
material change specular SemiTrans 0.50
material change diffuse SemiTrans 0.65
material change shininess SemiTrans 0.53
material change opacity SemiTrans 0.66

# Orbital
material add Orbital
material change ambient Orbital 0.00
material change specular Orbital 0.50
material change diffuse Orbital 0.65
material change shininess Orbital 0.53
material change opacity Orbital 0.38


############################################################################
# Working PATHs
############################################################################

set ARCH [vmdinfo arch]

# default $env(HOME)
# windows C:\Documents and Settings\jianzou
# linux /home/jianzou

# default $env(VMDDIR)
# windows d:/Program Files/University of Illinois/VMD
# linux /home/jianzou/program/vmd

if { ! [string compare -nocase $ARCH "WIN32"] } {
   set env(HOME) "d:/Program Files/University of Illinois"
} elseif { ! [string compare -nocase $ARCH "LINUX"] } {
   set env(HOME) "$env(HOME)/program"
} else {
   puts "wrong ARCH"
   exit
}

# molfile plugins in $env(VMDDIR)/plugins/$VMDARCH/molfile
# 'vmdinfo arch' --> $VMDARCH
# 'file join /foo bar' --> /foo/bar
# 'array get env' --> $env(index)
vmd_plugin_scandirectory [file join $env(VMDDIR)/plugins $ARCH molfile] *.so

# add scripts to the search path
# auto_path=$env(VMDDIR)/vmd/scripts/tcl:$auto_path
set auto_path [concat "$env(VMDDIR)/scripts/tcl8.4" $auto_path]

# source command extensions (e.g. vmd_draw_vector)
foreach ext [glob -nocomplain $env(VMDDIR)/scripts/extensions/*.tcl ] {
   source $ext
}
unset ext


############################################################################
# Change the default VDW radii
############################################################################

proc my_set_def_vdw {args} {
lassign $args fname molid

set my_def_vdw {
   {name "C.*" } { 0.5 } \
   {name "OW" } { 0.3 } \
   {name "HW." } { 0.3 } \
}

foreach {selstr rad} $my_def_vdw {
   set my_sel [atomselect $molid "$selstr"]
   $my_sel set radius $rad
   $my_sel delete
}
}
trace variable vmd_initialize_structure(0) w my_set_def_vdw
trace variable vmd_initialize_structure(1) w my_set_def_vdw
trace variable vmd_initialize_structure(2) w my_set_def_vdw


############################################################################
# Misc.
############################################################################

# tkcon-menu popup
after idle {menu tkcon on}

# user-defined representation method
mol default color resid
mol default material Opaque
mol default selection "all"
mol default style {Bonds 0.3 15}
mol default style {VDW 0.3 15}
mol default style {CPK 0.9 0.4 15 15}
mol default style {HBonds 3.5 30 3}
mol default style {NewCartoon 0.3 6 4.1 0}

# User's default values for newly loaded molecules/reps, etc
mol default color {colorID 5}
mol default style {NewCartoon 0.300000 6.000000 4.100000 0}
mol default selection {name CA}
mol default material {Transparent}

VMD Resources

Visualization and Analysis of CPMD data with VMD
http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/index.html

Building Gramicidin A
http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/

TCBG VMD Tutorial
http://www.ks.uiuc.edu/Training/Tutorials

VMD Molecular Graphics
http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/index.html

VMD Images and Movies Tutorial
http://www.ks.uiuc.edu/Training/Tutorials/vmd-ref/imgmv/tutorial-html/index.html

Aquaporins with the VMD MultiSeq Tool
http://www.ks.uiuc.edu/Training/Tutorials/science/aquaporin/tutorial_aqp-html/index.html

TCBG Science Topics

http://www.ks.uiuc.edu/Training/Tutorials

Parameterizing a Novel Residue
http://www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/forcefield-html

Evolution of Biomolecular Structure: Class II tRNA-Synthetases and tRNA

Sequence Alignment Algorithms

Topology File Tutorial
http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-html

User-Defined Forces in NAMD
http://www.ks.uiuc.edu/Training/Tutorials/science/forces/forces-tutorial-html

Bionanotechnology Tutorial
http://www.ks.uiuc.edu/Training/Tutorials/science/bionano/bionano-tutorial-html


Interactive Molecular Dynamics Tutorials
http://www.ks.uiuc.edu/Training

Brief introduction
http://www.ks.uiuc.edu/Research/vmd/imd/tutorial

Stretching Deca-Alanine
http://www.ks.uiuc.edu/Training/Tutorials/science/10Ala-tutorial/tutorial-html/index.html

Simulation of Water Permeation through Nanotubes
http://www.ks.uiuc.edu/Training/Tutorials/science/nanotubes/nanotubes-html/index.html

PMF and Water Channel

# water in hydrophobic nanopore
http://sbcb.bioch.ox.ac.uk/oliver/research/pores/hyphobpores.html


Links

Dr. Gerhard Hummer: water channels
http://intramural.niddk.nih.gov/research/faculty.asp?People_ID=1615

Dr. Oliver Beckstein: water & ion channels
http://sbcb.bioch.ox.ac.uk/oliver/home.html

Dr. Mark Sansom: ion channels
http://sbcb.bioch.ox.ac.uk/sansom.php

Dr. Petros Koumoutsakos: CNT and water
http://www.icos.ethz.ch/people/personal_data/petros

Dr. Markus J. Buehler
http://web.mit.edu/mbuehler/www/

Dr. Anton Feenston: Gromacs, Amber
http://www.few.vu.nl/~feenstra/

Dr. Axel Kohlmeyer: VMD-CPMD
http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/home.html

Dr. Peter Tieleman: membrane
http://moose.bio.ucalgary.ca/index.php?page=Peter_Tieleman

Dr. Shigeo Maruyama: CNT
http://www.photon.t.u-tokyo.ac.jp/~maruyama/index.html

GROMACS Resources

GMX-wiki
http://wiki.gromacs.org/index.php/Main_Page

Souce code
http://www.gromacs.org/content/view/79/98/

On-line Manual
http://www.gromacs.org/component/option,com_wrapper/Itemid,192/

PRODRG
http://davapc1.bioch.dundee.ac.uk/programs/prodrg/

WHAM
http://membrane.urmc.rochester.edu/

ffAMBER
http://chemistry.csulb.edu/ffamber/
http://www.stanford.edu/group/pandegroup/folding/ffamber/index.html

Gromacs Workshop: 2007-02-26
http://tv.funet.fi/medar/showDirectory.do?directory=/metadata/fi/csc/courses/gromacs_workshop_2007

Free Energy: Tutorial - DillgroupWiki
http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial

Molecular Dynamics Tutorial (GROMACS)
http://md.chem.rug.nl/education/mdcourse/

QM-MM
http://www.rug.nl/gbb/research/researchgroups/molecularDynamics/index

MARTINI Forcefield: Coarse-Grained Lipid Model
http://md.chem.rug.nl/~marrink/coarsegrain.html

PyMOL free release is obsolete

pymol@sf.net
http://sourceforge.net/project/showfiles.php?group_id=4546

The last free release
http://delsci.com/rel/099/

manual
http://pymol.sourceforge.net/html/

Molecular Modeling

EMBO 2004
http://www.dddc.ac.cn/embo04/

TCBG Tutorial
http://www.psc.edu/general/software/alphabetical/alphabetical.html

PSC: Pittsburg Supercomputing Center
http://www.psc.edu/general/software/packages/
http://www.psc.edu/general/education/education.html
http://www.psc.edu/general/software/alphabetical/alphabetical.html

Structural Bioinformatics
http://www2.umdnj.edu/~kerrigje/structbio_II.htm

Macromolecular Visualization
http://www.chem.ucsb.edu/~kalju/chem110L/public/tutorial/start.html


Visualization resources

Projects
http://openil.sourceforge.net/projects.php

Vega
http://users.unimi.it/~ddl/

netpbm
http://netpbm.sourceforge.net/


Topology

Hetero-compound Information
http://alpha2.bmc.uu.se/hicup/

PRODRG
http://davapc1.bioch.dundee.ac.uk/programs/prodrg/

outstanding attendance!

今天中午，Jill的课上，Lisa叫我上讲台，代表学校向我颁发了一纸贺卡，Id card还有一些coupon，对我极高的上课出勤率给予嘉奖。呵呵。好久没有站在讲台上享受领奖的感觉了，当台下掌声四起的时候，内心的虚荣心得到了极大的满足啊！我禁不住想起了“见荣王”，哈哈哈。

Nanotube Resouces

Physical Properties of Carbon Nanotubes
http://www.pa.msu.edu/cmp/csc/ntproperties/

Fullerene Structure Library
http://www.cochem2.tutkie.tut.ac.jp/Fuller/fsl/fsl.html

Shigeo Maruyama's CNY and Fullerene site
http://www.photon.t.u-tokyo.ac.jp/~maruyama/nanotube.html

Nanomechanics: REBO code
http://www.mse.ufl.edu/~ssinn/sub05b_nanomechanics.html

Nano-Gear
http://www.somewhereville.com/?page_id=10
http://www.nanoengineer-1.net/mediawiki/index.php?title=Tutorial:_Simulating_the_NASA_NanoGear

CoNTub
http://www.ugr.es/~gmdm/contub.htm

一些查材料参数的地方 (ZZ)

发信人: wsjxaut (没籽的葡萄好吃), 信区: FEA
标 题: 一些查材料参数的地方
发信站: 水木社区 (Thu Aug 17 22:26:30 2006), 站内

忘了从哪里弄来的了,好像是simwe

GENERAL:
http://www.matweb.com/
http://www.tc.faa.gov/its/worldpac/techrpt/ar-mmpds-01.pdf
http://femci.gsfc.nasa.gov/links.html
http://www.azom.com/
http://www.asme.org/index.html
http://www.intlmag.org/mechanical.aspx
http://www.mpif.org/
http://www.namtec.co.uk/metals/
http://www.steelynx.net/
http://www.machinedesign.com/ASP/enggMaterial.asp?catId=372

Fatigue:
http://femci.gsfc.nasa.gov/links.html
http://www.engineering-e.com/datamart/
http://www.ductile.org/didata/default.htm

Metalforming:
http://www.a-sp.org/database/publicationmain.asp

Plastics:
http://matdata.net/index.jsp
http://www.materialdatacenter.com/materialdatacenter/matdb/matdb.php
http://iwww.plasticsportal.com/products/products.html
http://www.geplastics.com/resins/techsolution/designguide.html

Vibro-Acoustics:
http://www.nvhmaterials.com/nvh/Materials/index.htm
http://www.saecollege.de/reference_material/pages/Coefficient%20Chart.htm
http://hyperphysics.phy-astr.gsu.edu/hbase/acoustic/revmod.html#c4

Free Plotting Tools

Grace
http://plasma-gate.weizmann.ac.il/Grace/

WinDIG
http://www.unige.ch/sciences/chifi/cpb/windig.html

LabPlot
http://labplot.sourceforge.net/index.html

Open Directory
http://www.dmoz.org/Science/Math/Software/Graphing/

QtiPlot
http://www.opendesktop.org/content/show.php/QtiPlot?content=14826

gnuplot: tips

gnuplot;gt plot "plot_dih.dat"

set data style lines linespoints, impulse, boxes
replot

set xrange [min to max]
set yrange [min to max]
set autoscale

plot "datafile" u x_row:y_row title "title"
plot "dat1" u x1:y1 title "t1", "dat1" u x1:y1 title "t1"

set terminal postscript
set terminal postscript color solid "Helvetica" 10
set output 'dih.ps'
replot

QtiPlot Installation

Installation Notes
http://soft.proindependent.com/install.html

0. Prerequisite (with -devel)
Qt .gt. 4.2
GSL
zlib

1. Qwt .gt. 5.0.0
cd qwt
qwtconfig.pri: comment out "CONFIG += QwtDll"
qmake
make

2. QwtPlot3D
cd qwtplot3d
qwtplot3d.pro: add the line "CONFIGU += staticlib"
qmake
make

3. muparser
./configure --enable-shared=no --prefix
make
make install

4. qtiplot
cd qtiplot
qmake
make

Grace Tips

# header
# This file was created for grace
#

@ title ""
@ xaxis label ""
@ yaxis label ""
@ s0 legend ""
@ s1 legend ""
@ xaxes scale Logarithmic
@ yaxes scale Normal

# subscript
x\si\N

# superscript
x\S2\N


Toolbar

Draw: Redraw

Lens: Zoom lens
AS: AutoScale

Z/z: Zoom in/out

Arrows: Scroll active graph

AutoT: AutoTick Axes.

AutoO: Autoscale On "set"

ZX,ZY: Zoom only along X/Y axis
AX,AY: Autoscale one axis only.

Pu/Po: Push and pop to/from the graph stack
PZ: Push before Zooming
Cy: Cycles through the stack settings

Exit


hotkey

# Canvas hotkeys
Ctrl-A Autoscale
Ctrl-L Move legend
Ctrl-U Update
Ctrl-Z Zoom

# Draw on canvas
Ctrl-Alt-L Draw a line
Ctrl-Alt-B Draw a box
Ctrl-Alt-E Draw a ellipse
Ctrl-Alt-T Draw a text string

Ctrl-D Delete an object
Ctrl-M Move an object

# List selectors
Ctrl-A select all
Ctrl-U unselect all
Ctrl-I invert selection


Installation

4.3 When I run `configure', it says the XXX package is not found, whereas I am certain it was installed on my system!
There are several possible reasons:
* You have only the run-time part installed (this especially concerns GNU/Linux users). However, you should have the relevant development package (C header files etc) installed, too. E.g., for the JPEG library to be recognized by `configure', both libjpeg62 and libjpeg62-devel packages must be installed.
* The library and the header files don't match each other (they are from different versions). This usually happens on large Unix systems with a less than capable sysadmin...
* Either the library or the header files can't be found by the compiler. Use the --with-extra-ldpath and --with-extra-incpath configure options to provide the extra paths, respectively.

4.4 When I type './configure' I get: ``configure: error M*tif has not been found''
Check whether M*tif (question M*tif) is installed on your system. If it is, look at the file config.log: there is a line like this:
configure:8900: checking for a Motif >= 1002 compatible API
What comes directly after it? Could be a hint. Also, see the previous question.

The configure for grace is looking for a Motif compatible
library, not for a Windowing software. Motif and Lesstif are
both refering to the Windowing software and the name of the
library. Lesstif is probably installing a Motif compatible
library as well, possibly from openmotif. The required
library is libXm.a (static) or libXm.so (shared).
The usual place for this library is in /usr/X11R6/lib.
In case the configure does not find the required library,
it is necessary to instruct it to look in the correct place.
I use the following prefix to the configure in order to let
it know where to look for the required library and include files:

./configure --prefix=/sasbuild/local \
--enable-grace-home=/sasbuild/local/grace_5.1.20 \
--with-extra-incpath=/sasbuild/local/fftw_2.1.3/include:/usr/X11R6/include/Xm \
--with-extra-ldpath=/sasbuild/local/fftw_2.1.3/lib \
--with-fftw-library=/sasbuild/local/fftw_2.1.3/lib/libfftw.a \
--with-motif-library=/usr/X11R6/lib/libXm.a

Look at the third line and the last one. The tell the configure to
look for includes for Motif in /usr/X11R6/include/Xm and for the
Motif compatible library in /usr/X11R6/lib/libXm.a.

The rest of the configure prefixes shown above are self-explanatory
and obviously allow us to build grace in a different directory to
the usual default which is /usr/local.

The configure command shown above is what I use in fact to build
our grace software. Notice that in our case we use the FFTW software
as well, as part of the building process for grace.

In case the Lesstif software does not include the Openmotif library,
you can download the Openmotif package or build it from source code
as well.

I hope this helps you to find out the way to build grace from source
code.

冷漠

你知道什么是冷漠吗？你尝过被人冷漠的感觉吗？昨晚发现自己哭不出来了，想哭但是哭不出来的感觉真的很难受，我有些怀念自己可以痛痛快快哭泣的感觉。好久好久睡不着，不知是不是白天睡得太多了，胡思乱想没有头绪。外面很吵，铲雪车的运作打破了深夜的寂静，头痛欲裂。看着他背过身去，原来如此温暖地方也可以瞬间如此冰凉...有时候真的什么都不要说，也什么都不用再说了。

Endnote 小技巧

# Web of Science
Thomson Scientific was known as the Institute for Scientific Information (ISI, 美国科学情报研究所).


How to export from Web of Science

1. Most important fields
Author Title Source
ISSN
source abbrev.
keywords
Alternative Journal

# do not use
abstract
cited references
IDS number

Biblio wo Alter Journal
Full Record wi Abstract


search example

TI=(Single-molecule torsional pendulum) OR RETURN
TI=(Nanoscale carbon nanotube motor schematics and simulations for micro-electro-mechanical machines) OR RETURN
(TI=(Nanotechnology - Beyond Gedanken experiments) AND AU=Forro)

Online Scientific Topics

resources

http://www.integral-table.com/

PlanetMath
http://planetmath.org/

TCAEP
http://www.scenta.co.uk/tcaep/

Mathtools.net: Link Exchange
http://www.mathtools.net/


online courses: Chinese

复变函数
http://math.fudan.edu.cn/teacher/123/guid0.htm

量子力学
http://qm.phys.tsinghua.edu.cn/qm

数理方程
http://www2.phy.pku.edu.cn/%7Emmp/download/?PHPSESSID=d40fc839cf8e68b11e515d15e788179b

中科大数学建模站
http://mcm.ustc.edu.cn/download.htm


online courses: English

Bio Chemistry
http://www.web.virginia.edu/Heidi/chapter1/chp1.htm

Lehninger Principles of Biochemistry: online book
http://bcs.whfreeman.com/lehninger/default.asp?s=&n=&i=&v=&o=&ns=0&uid=0&rau=0

Polymer Science
http://gozips.uakron.edu/~mattice/ps674/dir.html

Safari: Online Books
http://proquest.safaribooksonline.com

Virtual Text: Gene VII
http://virtualtext.jbpub.com/index.jsp

HyperPhysics Concepts
http://hyperphysics.phy-astr.gsu.edu/hbase/hph.html

eFluids: Educational Tools and Materials
http://www.efluids.com/efluids/pages/edu_tools.htm

Asiaing.com: Free eBooks, Free magazines, Knowledge sharing
http://www.asiaing.com/

Online books
http://gigapedia.org/

Prefix: order of magnitudes

10E+48 ultra
10E+45 quinsa
10E+42 cata
10E+39 astra
10E+36 vela
10E+33 besa
10E+30 sansa
10E+27 nava
10E+24 yotta
10E+21 zetta
10E+18 exa
10E+15 peta
==========
10E+12 tera
10E+09 giga
10E+06 mega
10E+03 kilo
10E−03 milli
10E−06 micro
10E−09 nano
10E−12 pico
10E−15 femto
10E−18 atto
==========
10E−21 zepto
10E−24 yocto
10E−27 tiso
10E−30 vindo
10E−33 weto

Viscosity of Water

The viscosity of water at room temperature is roughly 1 centipoise, or 1 cP. Gasoline has a viscosity between 0.4 and 0.5 cP; the viscosity of air is 0.018 cP.

cP (centipoise) = 10-2 poise = 10-3 Pa*second = 10-3 kg/m*s

poise = dyne * second / cm^2 = 10-1 Pa*sec = 10-1 N/m^2*s = kg/m*s
dyne = g * cm/ sec^2 = 1E-5 newton (kg*m/s^2)


cf.
http://www.ce.utexas.edu/prof/kinnas/319LAB/Book/CH1/PROPS/dynviscgif.html
http://chemed.chem.purdue.edu/genchem/topicreview/bp/ch14/property.php#viscosity