Hi
Could someone indicates me a program or script to create an all-to-all RMSD map computed from molecular dynamics trajectory?
I want to generate a correlation map between the RMSD of the amino acid residues of a protein from the molecular dynamics trajectory file, as described in figure 2 of this reference:
https://www.livecomsjournal.org/article/5067-best-practices-for-quantification-of-uncertainty-and-sampling-quality-in-molecular-simulations-article-v1-0
I know that UCSF Chimera program does this map, however, it does not allow me to align given regions of the protein (chains or residues) and calculate rmsd for other regions.
The VMD program has a plugin called RMSD Visualizer tool, which does the alignments and calculates the rmsd for the same or distinct regions, however, it does not generate the RMSD map.
http://mdtraj.org/1.9.0/
This program might be useful. However, VMD can generate data file from your trajectory, which can be utilized for desired plotting by external statistical software.
or
http://thegrantlab.org/bio3d/tutorials/protein-structure-networks
this program can help you to get your result towards scripting
Hi Flavio,
I am not sure which program are you using for MD simulation, however, if you use GROMACS then you could use the following link to help you construct the RMSD plot that you desire.
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Molecular_Dynamics_Simulations_Analysis_of_Glucocerebrosidase
PS - I would recommend you to go for simple line plot instead of such a fancy plot. It might be challenging for you to explain the data and might also be tricky for your potential reader to grasp those details easily.
Have you tried CONAN?
Article CONAN: A Tool to Decode Dynamical Information from Molecular...
https://www.plumed.org//
PLUMED is an open-source tool can be used to analyze MD data
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