Computer Lab 1
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The computer lab consists of two separate parts. The goal for both of them is to give a glance at what molecular dynamics simulations can be used for, but also to enable you to see some of the theoretical concepts we've discussed during the seminars in practice - because the theory does hold! Note that we had to limit ourselves to small systems and short time scale processes. Larger systems and long time scale processes can be (and are) studied using molecular dynamics simulations but they require much more time.
In the first part, you will work with small systems containing various peptides in a water box and observe how these peptides fold (or not) into alpha-helices. You will learn how to build such a system, run minimization and molecular dynamics simulations. You will also learn how to visualize molecular dynamics trajectories and how to perform analysis of those trajectories using python.
We recommend that you work in pairs.
Since the KTH desktop computers in the RB33 room are quite old/slow, not to mention that they only have Windows installed, on popular demand we have instead moved to using your laptops and installing the software natively - this will be much faster and smoother compared to running Ubuntu in a virtual image, in particular when using VMD for visualization.
We basically use three pieces of software: GROMACS (for running simulations), VMD for visualization, and PYTHON/MDTRAJ for analysis and plotting.
You can find detailed software installation instructions for a number of different platforms and options through the Google drive link:
https://drive.google.com/drive/folders/1dRoSOfsjGlPl9LM9TDVmv7uyUNl0Qhj8
Links to an external site.
Short URL if you need to type this into a browser on a different computer: https://shorturl.at/dMh51
Links to an external site.
... and here is a copy of the software installation guide. Download software installation guide.
If you have problems with installing the software, please post questions at Ask a Question so others that have the same issue can also find or post solutions.
To keep things organized, it is good to run each lab in a separate subdirectory. If you simply unpack the the relevant input files with
tar -xzvf sk2534_lab1.tar.gz
then you will automatically get the contents in a directory called sk2534_lab1 (and correspondingly for lab2).
No report is needed. During the lab we will ask you various questions (from the attached PDF) to check your progress.
If you absolutely can't attend, you will be allowed to do the lab on your own, but then the requirement will be a written report instead. Contact the teachers to arrange this!
Instructions: sk2534_lab1.pdf Download sk2534_lab1.pdf
Input files: sk2534_lab1.tar.gz Download sk2534_lab1.tar.gz
If you are using Windows, it might be easier to use this zip file version instead: sk2534_lab1.zip Download sk2534_lab1.zip
(You can unpack this by clicking on it in Windows, but make sure you get the files in the right place)
For the virtual machine we have already updated all software, but if you are running an older version of Ubuntu you might be influenced by a bug in release 2020 or 2021 of the GROMACS program. The step "gmx pdb2gmx" unfortunately generates bad output, and the conf.gro output should be replaced by the correct file below. Apologies for the inconvenience if this happens to you!
If you absolutely cannot install mdtraj, use there plots and explain what they mean:
ala-16
ala15-gly
ala15-pro
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