Blog Posts

Upgrading to the next Ubuntu LTS

7/19/2021

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

0 Comments

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

7/18/2021

1 Comment

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

1 Comment

MSD calculation with error bars using GROMACS

12/4/2020

10 Comments

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

10 Comments

How to continue running ssh processes even if connection drops.

11/5/2020

0 Comments

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

0 Comments

iOS and Android app for remote connections

9/8/2020

0 Comments

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

0 Comments

ACS Reviewer Lab

8/27/2020

0 Comments

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

0 Comments

Tips for creating nice images with VMD

4/25/2019

0 Comments

For nice images of proteins in VMD we recommend that you use the Graphics -> Representations -> Drawing Method -> Surf or MSMS visualisation, and then use the "Display -> Display Settings -> Ray Tracing Options -> Amb. Occl -> on" feature.

Here you can download MSMS:
http://mgltools.scripps.edu/downloads#msms

To render:
# smaller render, no normalization, high aasamling
[tachyonpath] -res 1920 1080 -aasamples 36 -add_skylight 1.0 %s -format PSD48 -o %s.psd

# huge render, high aasamling
[tachyonpath] -res 12460 9620 -aasamples 36 -add_skylight 1.0 %s -normalize -format PSD48 -o %s.psd

# below command can be used to set resolution when you don't want to force a resolution in tachyon
display resize 1280 1024

0 Comments

Free webinar by Christopher Lipinski on the Lipinski rules of 5

9/5/2018

0 Comments

Join Christopher Lipinski and Barry Bunin for a discussion on the "Lipinski Rules of 5," which has become the benchmark by which almost all drug discovery analyses are now compared.

Register here: https://info.collaborativedrug.com/lipinski-bunin-ruleof5-0-0

Experts will discuss:

Advanced drug discovery & data screening methods
What is the Lipinski Rule of 5 & How you can go beyond the Rule of 5 to achieve better results
New technologies to better assess the quality of your screening data
Experimental culture and sociology as a factor in clustering your results
How scientists can (and should) respond to the growing opioid addiction crisis – which has actually lowered life expectancy in America

0 Comments

How to display an Electron Density Map in Pymol

3/27/2018

1 Comment

Very often protein crystallography results in ambiguous regions of electron density.

To check that your protein structure is adequately represented by electron dements maps please see the following tutorial in pymol.

Zoe

1 Comment

How to create high quality figures with VMD

3/15/2018

4 Comments

In order to create high quality figures with VMD, go to: File > Render and use the Tachyon module in the File Render Controls panel.

Also, in order to increase the resolution of the figure, go to Render Command, in the same panel, and add the flag: -res xxx yyy, defining the number of pixels of the image.

Example:
"/usr/local/lib/vmd/tachyon_LINUXAMD64" -aasamples 12 %s -format TARGA -res 1600 1200 -o %s.tga

Christina

4 Comments