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Date: Tuesday, 03 Mar 2009 02:24

The density calculator, interpolation.

Author: "--" Tags: "links"
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Date: Sunday, 01 Mar 2009 07:22
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Date: Sunday, 01 Mar 2009 07:12
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Date: Sunday, 01 Mar 2009 07:10

Author: "--" Tags: "links"
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OO'd CSS   New window
Date: Sunday, 01 Mar 2009 06:46
Author: "--" Tags: "links"
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Date: Saturday, 15 Nov 2008 20:20
Author: "--" Tags: "links"
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Date: Thursday, 13 Nov 2008 10:01
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Author: "--" Tags: "politics"
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Date: Tuesday, 03 Apr 2007 00:03

via random google search result:

"Single Precision occupies 32 bits (4 bytes) and has a significand precision of 24 bits. This gives it an accuracy of about 7 decimal digits.
Double precision occupies 64 bits (8 bytes) and has a significand precision of 53 bits. This gives it an accuracy of about 16 decimal digits."

Todo: review the floating point part of the computor architecture textbook

Author: "--" Tags: "science"
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Date: Thursday, 21 Dec 2006 01:23


- via random flickr search.

Author: "--" Tags: "image"
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Date: Thursday, 21 Dec 2006 01:18


- via random flickr search.

Author: "--" Tags: "image"
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Date: Thursday, 21 Dec 2006 01:06


- via random flickr search.

Author: "--" Tags: "image"
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Date: Monday, 04 Dec 2006 04:47
From now on, all my notes on find(1) go here.
$ find . -not -iname '*gz' -size +50000 -atime +30 -print0 | xargs -0 gzip -9
Author: "--" Tags: "nerd"
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Date: Thursday, 09 Nov 2006 03:31

For some reason, after I enabled the Dedicated Network Builds of Xcode, the dnbobserver will be always on, even after I disabled the DNB later in the preferences. So here is how you can do to tell launchd to stop running it.

#!/bin/bash
sudo launchctl unload -w /System/Library/LaunchDaemons/com.apple.dnbobserver.plist

Author: "--" Tags: "mac"
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Date: Monday, 06 Nov 2006 22:40
Although this functionality has been in the posix standard for awhile, your mileage might vary.
      program main
      call system('sysctl vm.swapusage')
      end program main
(tested on g95, intel fortran)
Author: "--" Tags: "nerd"
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Date: Tuesday, 31 Oct 2006 09:33

AMBER_SRC=~/amber9/src
AMBERBUILDFLAGS=
LOCALFLAGS=
USE_BLASLIB=$(VENDOR_SUPPLIED)
USE_LAPACKLIB=$(VENDOR_SUPPLIED)
USE_LMODLIB=$(LMOD_UNAVAILABLE)
CC= gcc
CPLUSPLUS=g++
CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -m32
CPPFLAGS= $(AMBERBUILDFLAGS)
FPPFLAGS= -P -xassembler-with-cpp -DHASSECOND $(AMBERBUILDFLAGS)
FPP= cpp -traditional $(FPPFLAGS)
FC= g95
FFLAGS= -O0 -fno-second-underscore $(LOCALFLAGS) $(AMBERBUILDFLAGS)
FOPTFLAGS= -O3 -fno-second-underscore $(LOCALFLAGS) $(AMBERBUILDFLAGS)
FREEFORMAT_FLAG= -ffree-form
LOAD= g95  $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADCC= gcc  $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADLIB=-Wl,-framework -Wl,Accelerate
LM= -lm
LOADPTRAJ= g95 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
XHOME= /usr/X11R6
XLIBS= -L/usr/X11R6/lib
#------------------------------------------------------------------------------
#  Other stuff:
#------------------------------------------------------------------------------
.SUFFIXES:  .f90
EMPTY=
AR=ar rv $(EMPTY)
M4=m4
RANLIB=ranlib
SFX=
NETCDF=
NETCDFLIB=
MODULEDIR=-I
MAKEDEPEND=$(AMBER_SRC)/../bin/amber_makedepend
SLKO=skipDFTB

#  default rules for Fortran and C compilation:

.f.o:   $$<
        $(FPP) $$< $> _$$<
        $(FC) -c $(FFLAGS) -o $@ _$$<

.c.o:   
        $(CC) -c $(CFLAGS) $(CPPFLAGS) -o $@ $<

Author: "--" Tags: "simulation"
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Date: Monday, 16 Oct 2006 19:45

Salt bridges can be treated as the neutralization of an acid and amine on side chains. To be exact, it's the ionic interaction between the positive ammonium group (ASP, GLU) and the negative acid group (LYS, ARG and protonated HIS). A this kind of interaction is defined if the charged groups are less than or equal to 4.0 angstroms apart (Barlow and Thornton, 1983).

The ptraj manual doesn't provide details about the rule of mask, but the source code does have sufficient information for me to continue.

#!/bin/sh
ptraj(){
   ${AMBERHOME}/exe/ptraj prmtop << EOF
trajin md.trj.gz
checkoverlap (:LYS@NZ|:ARG@NE,NH1,NH2|:HIP@NE2) min 4.0 noimage around (:GLU@CD|:ASP@CG)
go
EOF
# Barlow DJ and Thornton JM, "Ion-pairs in proteins", (1983)  J Mol Biol.;168(4):867-85.
# However instead of (:GLU@OE1,OE2|:ASP@OD1,OD2) on this paper, we use the definition
# that is less generous (:GLU@CD|:ASP@CG).....
}
ptraj | perl -p -e 's/\.OVERLAP/\nOVERLAP/g;s/ OVERLAP/\nOVERLAP/g' \
        | awk '/are too close/{print $5,$10}'  > log

Author: "--" Tags: "simulation"
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Date: Thursday, 05 Oct 2006 23:34

The X11 package that comes with Mac OS X has been causing some kind of annoyances related to ssh -Y and X11 tunneling. It looks like this warning message:

[Powerbook:~] mjhsieh% ssh -Y localhost
Warning: No xauth data; using fake authentication data for X11 forwarding.
And I have been trying to tell xauth to work with me but failed all the time. Hooray! Finally this works:
[Powerbook:~] mjhsieh% xauth generate :0 .
Please be noted that this command should be used every time you gain a new IP....

Author: "--" Tags: "mac"
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Date: Friday, 15 Sep 2006 10:39

After version 1.8.5, VMD can automatically guess file types base on the filename extension. According to the molfile plugin for VMD, you need to use prmtop or parm7 for the filename extension of parm7 format. Also rst7 for the filename extension for rst7 format. With these filename suffix, you can save some time selecting the file type. Too bad we don't have inpcrd for the rst7 (without velocity), I'll check the source later. :-)

mdcrd, crd is for the trajectory (AMBER Coordinates)
crdbox for trajectory with box information (AMBER Coordinates with Periodic Box)

Author: "--" Tags: "simulation"
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Date: Friday, 15 Sep 2006 07:36

Just cd to /usr/share (205781 files) and issue the command (under bash):

echo `find .` > /dev/null
Check this out.

Author: "--" Tags: "nerd"
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Date: Friday, 25 Aug 2006 04:07

amber
(Original: 2002-12-08, Updated 2003-06-06) Forgot to store some important information. I extracted the table from amber's manual, hopefully it helps me.

----
Group or residueResidue Name
----
Acetyl beginning groupACE
Amine ending groupNHE
N-methylamine ending groupNME
AlanineALA
ArginineARG
AsparagineASN
Aspartic acidASP
Aspartic acid, protonatedASH
CysteineCYS
Cystine, S--S crosslinkCYX
Glutamic acidGLU
Glutamic acid, protonatedGLH
GlutamineGLN
GlycineGLY
Histidine, delta HHID
Histidine, epsilon HHIE
Histidine, protonatedHIP
Histidine, metal(?)HIM
IsoleucineILE
LeucineLEU
LysineLYS
MethionineMET
PhenylalaninePHE
ProlinePRO
SerineSER
Serine, phosphorylatedSEP
ThreonineTHR
TryptophanTRP
TyrosineTYR
ValineVAL
----
Author: "--" Tags: "simulation"
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