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Updating Ubuntu packages

12/15/2021

sudo apt-get update

sudo apt-get clean

sudo apt-get update

sudo apt-get upgrade

sudo apt-get dist-upgrade

You can also try:
sudo apt full-upgrade

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Ubuntu 20.04 start screen frozen at system check (Ctrl-C to stop system checks does not work)

12/15/2021

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1) Install the recommended NVIDIA drivers for your graphics card:

sudo add-apt-repository ppa:graphics-drivers/ppa

ubuntu-drivers devices

sudo apt install [driver_name]
or
sudo ubuntu-drivers autoinstall

sudo reboot

2) you may have to uninstall all nvidia drivers first

dpkg -l | grep -i nvidia

sudo apt-get remove --purge '^nvidia-.*'

sudo apt-get install ubuntu-desktop

sudo reboot

3) Disable nvidia-drm modeset option

I discovered that prime-select writes a configuration file which causes the problem. It enables the nvidia-drm modeset option. You can simply undo the change made by prime-select by commenting out this option. It will not be reset, because prime-select only writes this file when it does not exist yet."
Open the file in your favorite editor (vim, nano, gedit, etc.).
sudo nano /lib/modprobe.d/nvidia-kms.conf And comment out the the nvidia-drm modeset option.
# This file was generated by nvidia-prime # Set value to 0 to disable modesetting # options nvidia-drm modeset=1

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LiPyphilic: A Python Toolkit for the Analysis of Lipid Membrane Simulations

8/30/2021

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LiPyphilic is a Python package for analyzing such simulations. Analysis tools in LiPyphilic include the identification of cholesterol flip-flop events, the classification of local lipid environments, and the degree of interleaflet registration. LiPyphilic is both force field- and resolution-agnostic, and by using the powerful atom selection language of MDAnalysis, it can handle membranes with highly complex compositions. LiPyphilic also offers two on-the-fly trajectory transformations to (i) fix membranes split across periodic boundaries and (ii) perform nojump coordinate unwrapping. Implementation of nojump unwrapping accounts for fluctuations in the box volume under the NPT ensemble—an issue that most current implementations have overlooked. The full documentation of LiPyphilic, including installation instructions and links to interactive online tutorials, is available at https://lipyphilic.readthedocs.io/en/latest.

Publication can be found here: https://pubs.acs.org/doi/10.1021/acs.jctc.1c00447

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Mounting a new disk on Ubuntu - permissions

7/22/2021

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When mounting a new disk on Ubuntu the default permissions are:
rw,nosuid,nodev,noexec,relatime

which don't allow one to execute programs.

The solution is to remove the 'noexec' option with

noexec με mount -o remount,rw,nosuid,nodev,relatime /media/mydata3

Alexis

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Upgrading to the next Ubuntu LTS

7/19/2021

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You can jump between Ubuntu LTS versions but if you are not on the LTS you 'd have to first update to the next Ubuntu version.
Be sure to fully update your current OS:

sudo apt-get update
sudo apt-get upgrade

Then try 'sudo apt install update-manager-core' to check for any broken dependencies
Fix any broken problems, usually by removing them and re-installing them.

sudo shutdown -r now
Then, sudo do-release-upgrade

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Textbook for Teaching Scientific Computing to Chemistry Students with Python and Jupyter Notebooks

7/18/2021

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This book is written to teach the subject using Python, Jupyter notebooks, and the SciPy stack which are all open source and cross-platform software; the text assumes no previous computer programming background from the students. The textbook is an open educational resource released under the CC BY-NC-SA 4.0 Creative Commons license and can be freely downloaded at https://github.com/weisscharlesj/SciCompforChemists together with related material.

The article below provides descriptions and philosophy behind the structure and content of the book along with insights and advice based on its use in an undergraduate course: https://pubs.acs.org/doi/10.1021/acs.jchemed.0c01071

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MSD calculation with error bars using GROMACS

12/4/2020

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To compute the MSD with error using GROMACS use the gmx analyze command:
http://manual.gromacs.org/documentation/5.1/onlinehelp/gmx-analyze.html

For error bars in a single trajectory (block averaging) use the -ee option:

"Option -ee produces error estimates using block averaging. A set is divided in a number of blocks and averages are calculated for each block. The error for the total average is calculated from the variance between averages of the m blocks B_i as follows: error^2 = sum (B_i - <B>)^2 / (m*(m-1)). These errors are plotted as a function of the block size."

The command line is:
gmx analyze -f msd_all_DPPC.xvg -ee err_dppc

Error bars can also be added with the option -errbar, but only if you have multiple replicas of the same system. The errorbars can represent the standard deviation.

The command line is:
gmx analyze -f msd_all_DPPC.xvg -ee err_dppc -errbar stddev

Sofia

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How to continue running ssh processes even if connection drops.

11/5/2020

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Have you ever faced the situation where you perform a long-running task on a remote machine, and suddenly your connection drops, the SSH session is terminated, and your work is lost. Well, it has happened to all of us at some point, hasn’t it? Luckily, there is a utility called screen that allows us to resume the sessions.

Screen or GNU Screen is a terminal multiplexer. In other words, it means that you can start a screen session and then open any number of windows (virtual terminals) inside that session. Processes running in Screen will continue to run when their window is not visible even if you get disconnected.

The screen package is pre-installed on most Linux distros nowadays.

More information and how to use it is here:

https://linuxize.com/post/how-to-use-linux-screen/

Alexis

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iOS and Android app for remote connections

9/8/2020

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Hello all,

Using the app: https://termius.com/

you can connect with ssh to any linux machine (it's a similar app to e.g. Putty in a Windows PC) . So you can connect to your lab desktop and through it you can ssh to a supercomputer or any server you are using to submit/monitor jobs and run any terminal commands you need.

Sofia

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ACS Reviewer Lab

8/27/2020

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The following tutorial is designed to help you learn how to become a journal reviewer. It is highly recommended as you 'll also learn how reviewers think, so you can better prepare your own manuscripts. It only takes 2-3 hours and it's free.

As a Bonus, a certificate is issued if you answer correctly an easy assessment at the end of the tutorial!

https://www.acsreviewerlab.org/

Alexis

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<<Previous

Updating Ubuntu packages

Ubuntu 20.04 start screen frozen at system check (Ctrl-C to stop system checks does not work)

LiPyphilic: A Python Toolkit for the Analysis of Lipid Membrane Simulations

Mounting a new disk on Ubuntu - permissions

When mounting a new disk on Ubuntu the default permissions are:
rw,nosuid,nodev,noexec,relatime

which don't allow one to execute programs.

The solution is to remove the 'noexec' option with

noexec με mount -o remount,rw,nosuid,nodev,relatime /media/mydata3

Alexis

Upgrading to the next Ubuntu LTS

Textbook for Teaching Scientific Computing to Chemistry Students with Python and Jupyter Notebooks

MSD calculation with error bars using GROMACS

How to continue running ssh processes even if connection drops.

iOS and Android app for remote connections

ACS Reviewer Lab

Alexis, Isidora, Michalis, Danai, Panos, Celia, Klea, Zoe

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Categories

When mounting a new disk on Ubuntu the default permissions are:rw,nosuid,nodev,noexec,relatimewhich don't allow one to execute programs.The solution is to remove the 'noexec' option with​noexec με mount -o remount,rw,nosuid,nodev,relatime /media/mydata3Alexis

Alexis, Isidora, Michalis, Danai, Panos, Celia, Klea, Zoe

Archives

Categories

When mounting a new disk on Ubuntu the default permissions are:
rw,nosuid,nodev,noexec,relatime

which don't allow one to execute programs.

The solution is to remove the 'noexec' option with

noexec με mount -o remount,rw,nosuid,nodev,relatime /media/mydata3

Alexis