I'm new to Gromacs (and protein-analysis coding in general, but have some experience with python-based code). I'm trying to convert a .ene file received from pyDock to a more readable format (it currently opens
When I try to use different commands that the gromacs guide says accept .ene files (gmx eneconv and gmx dump), for example
gmx eneconv -f project.ene -o converted.edr
and
gmx dump -e project.ene -om read.mdp
I get the error
File 'project.ene' cannot be used by GROMACS because it does not have a recognizable extension.
The following extensions are possible for this option:
.edr
I have updated my OS and re-installed gromacs. My installation is working according to the 'Getting Started' page.
I am also open to suggestions for other programs to open and read the .ene file type.
Thanks!
"ene" is short for "energy" which contains binary data for energy, temperature, volume, etc, and is only used in older version of Gromacs. In new version of Gromacs this is replaced by "edr" file which contains portable binary data. See "gmx dump -h", you will find the following lines:
Options to specify output files:
-o [<.edr>] (fixed.edr)
Energy file
If you insist on using ene file, you should install an older version of Gromacs.
Related
I want to extract audio features from a large set of files using pyaudioanalysis, using the following command line (as suggested on the github project's page):
python3 audioAnalysis.py featureExtractionDir -i data/ -mw 1.0 -ms 1.0 -sw 0.050 -ss 0.050
This seems to indeed run the feature extraction - it takes time and return to prompt without error - but does not write any csv files.
Any hint about why this does not work would be greatly appreciated. Thank you.
Found the answer:
the files to be analyzed were actually ADPCM-compressed files, which apparently does not work. Therefore, this led to the following error (in the background, it was NOT returned, and only discovered while trying to run the command in a system call in R):
ValueError: Unknown wave file format: DVI_ADPCM. Supported formats: PCM, IEEE_FLOAT
Once files were uncompressed, the pyAudioAnalysis call worked as expected.
I rely a lot on core dumps for finding and fixing rare bugs on my personal applications.
I have multiple versions of my applications installed side by side, and decide which one to run (it depends on some other applications). Only one version of the same tool can run at any given time. My launchers start with "ulimit -c unlimited". When/if the application crashes, a core dump is generated.
One issue is that "file somecoredump" tells me the name of the process generated the core file, but I have no way to know which version of the application generated it, so it's not easy to tell which executable to use.
I'm wondering how this issue can be solved?
I can think of a couple of bad ways:
Embed the version info into the process name, such as MyProcess2.1c. Now "file corefile" tells me the version. Really ugly, I won't consider it.
Every launcher modifies /proc/sys/kernel/core_pattern and sets it to a path with the version info, such as /var/crash/2.1c/core. Ugly, because this setting affects all apps, not just mine. Also it only works now because I only allow a single version of the app to run at the same time, one day I might need to run multiple versions side-by-side.
What would be ideal for me is if there was a way to embed version info into the executable, and retrieve it from the core file. Is this possible?
You can use the strings command in linux to look for unique strings in a binary file. Perhaps you can compile the version into the binary such as this examnple from bash and then grep all the strings output to find it. Just prefix it with a unique string to make it easier to find?:
~]$ strings /usr/bin/bash | grep version
shell_version_string
build_version
sccs_version
rl_library_version
rl_do_lowercase_version
show_shell_version
rl_readline_version
dist_version
GNU bash, version %s-(%s)
GNU bash, version %s (%s)
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
#(#)Bash version 4.2.46(2) release GNU
display-shell-version
-l do not print tilde-prefixed versions of directories relative
HOSTTYPE The type of CPU this version of Bash is running under.
OSTYPE The version of Unix this version of Bash is running on.
version, type `enable -n test'.
do-lowercase-version
.gnu.version
.gnu.version_r
~]$
I am using pocketsphinx for offline speech recognition. I use lmtool to get language model and dictionary.But the language model has extension .lm but pocketsphinx requires .lm.bin file. So, how can I convert this?
You just need to:
1. Download http://sourceforge.net/projects/cmusphinx/files/sphinxbase/0.8/sphinxbase-0.8-win32.zip
Unpackage sphinxbase-0.8-win32.zip. The folder will be PATH\
In my case thats C:\Users\carope9\Desktop\
Move lm file to PATH\sphinxbase-0.8-win32\bin\Release
Open CMD and write cd PATH\sphinxbase-0.8-win32\bin\Release
Write sphinx_lm_convert -i YOUR_LM_FILE -o YOUR_LM.BIN_FILE
example: sphinx_lm_convert -i es_ES.lm -o es_ES.lm.bin
Your new lm.bin file will be into PATH\sphinxbase-0.8-win32\bin\Release
If you don't use Windows need to download source files from http://sourceforge.net/projects/cmusphinx/files/sphinxbase/0.8/sphinxbase-0.8.tar.gz but I don't know how to install it I'm reading https://sourceforge.net/p/cmusphinx/discussion/help/thread/c67930c0/?limit=25
P/D: According to some people this doesn't work, it worked for me and I don't know how to correct their error. Hope it helps you.
i want to make my own haar classifier for detection of hand, so i was following the toutorial given at
Naotoshi Seo. In this tutorial various linux command are used and i don't have linux.
some command are:
$ find [image dir] -name '*.[image ext]' > [description file]
$ createsamples -info samples.dat -vec samples.vec -w 20 -h 20
so how can i use these command on my windows
The "find" command creates a text file with the names of your image files. You can do that by hand if you want.
The second one is not a standard Linux command, but, I assume, one of the tools you need to create the classifier. If you want to use Windows you will have to download the Windows version of the tools in that tutorial. He uses Cygwin so you will need to install that as well.
Another option is to download the Ubuntu Live distribution and install it on a USB memory stick. You can then boot from the USB stick, create your classifier in Linux, then go beck to Widows when you're done.
I play to self-study 6.001 with the video lectures and lecture handouts. However, I have some problems setting up MIT Scheme in Ubuntu (intrepid).
I used package management and installed MIT-Scheme, but it's obviously the wrong version to use. It should be 7.5.1 instead of 7.7.90
I followed the instructions from this website (http://ocw.mit.edu/OcwWeb/Electrical-Engineering-and-Computer-Science/6-001Spring-2005/Tools/detail/linuxinstall.htm)
So far, I've downloaded the tar file, and extracted to /usr/local. I have no idea what step 3 means.
Then I entered command
scheme -large -band 6001.com -edit
and the error is
Not enough memory for this configuration.
I tried to run under sudo mode, and this time the error is different
Unable to allocate process table.
Inconsistency detected
I have close to 1GB of free memory, with ample HDD space. What should I do to successfully set this up?
Step 3 means that you should type export MITSCHEME_6001_DIRECTORY=${your_problems_path}. If you don't want to type it every time you launch Scheme, you should put it as a string in your ~/.bash_profile file(in case you use bash)
About the problem itself, Google instantly suggests a solution:
sudo sysctl -w vm.mmap_min_addr=0(taken from http://ubuntuforums.org/showthread.php?p=4868292)
Instead of the package manager, you may also want to compile the portable C sources for Unix. I am using it happily.