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Analysis of MD simulations using GROMACS tools

11/7/2012

5 Comments

 
I just came across this presentation which very nicely summarises the most important analysis tools for proteins available in Gromacs:  Definitely worth reading and very good as a reference for experienced gromacs users.

Analysis tools that you can find in the presentation include:
- Looking at your trajectory
- Groups in analysis
- Root mean square deviations and fluctuations
- Radius of gyration and distances
- Hydrogen bonds
- Secondary structure analysis
- Free energy surfaces
- Principal component analysis: using Cartesian coordinates or dihedral angles
- Clustering

Evi


5 Comments
what causes snoring link
8/21/2013 07:09:25 pm

I am pharmacy student and the post on molecular modeling and drug design was very informative for me. I understood many new things regarding the subject from this post. Keep up the good work guys. Waiting for more post.

Reply
beenish khurshid
10/20/2015 05:06:48 am

It was really helpful. thanks alot.

Reply
Bataa
12/9/2015 06:18:36 am

Hello, thank you for your presentation, I want to calculate FES same as your example. I have got following error.

command line:

python fes.py infilename minv1 maxv1 minv2 maxv2 devisions1 devisions2 310 outfilename

error message

File "fes.py", line 24
SyntaxError: Non-ASCII character '\xc2' in file fes.py on line 24, but no encoding declared; see http://www.python.org/peps/pep-0263.html for details

Reply
Ravi Rawat link
5/10/2021 09:55:36 am

HeroMDAnalysis is a tool for analysis of gromacs based MD simulation. Its free and support analysis of various parameters such as RMSD, RMSF, RoG, SASA, Free energy of Solv, H-bond contacts, Thermodynamic parameters, PCA Analysis. Its very simple, Graphical User Interface tool with no prior knowledge of command line interface required. Please visit www.heromdanalysis.wordpress.com for more information about this tool.

Reply
Edward C link
6/27/2022 01:07:44 am

Grreat reading this

Reply



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