Dear All
I have several MD trajectories generated by NAMD using coarse-grained dynamics. I would like to perform a deep analysis of the data. Is there any specific tool for this kind of analysis?.
Thanks in advance. Best
Paco
The coarse-grained reduction in complexity and resolution prevents you from computing many of the typical flexibility values. The NAMD forum provides a useful recipe: "There's the Bendix plugin for Coarse Grain result analysis (under the
visualization sub menu). This can help you for visualization and secondary
structure work. As for RMSD and Radius of gyration, you can simply use
the already existent RMSD tools and tcl interface in VMD. Just replace
your typical all atom selections with the appropriate coarse grained ones
(for example, instead of "name CA" or "backbone", use "name BAS" for CG
backbone RMSD calculations in the RMSD trajectory analyzer). "
Hi Karissa
I used Martini force-field simplification, meaning that each aminoacid is converted to two "atom-like" structures, one for the mainchain and other for the sidechain.
Best. Paco
Anything that can be simulated in NAMD can be analyzed in VMD (also from UIUC). The amount of in-house scripting you need to do depends on what you mean by "deep analysis."
The coarse-grained reduction in complexity and resolution prevents you from computing many of the typical flexibility values. The NAMD forum provides a useful recipe: "There's the Bendix plugin for Coarse Grain result analysis (under the
visualization sub menu). This can help you for visualization and secondary
structure work. As for RMSD and Radius of gyration, you can simply use
the already existent RMSD tools and tcl interface in VMD. Just replace
your typical all atom selections with the appropriate coarse grained ones
(for example, instead of "name CA" or "backbone", use "name BAS" for CG
backbone RMSD calculations in the RMSD trajectory analyzer). "
Thanks Ana... I will give a try to the Bendix plugin. In fact you pointed out all the main problems of the coarse grained simplification. Great post and great help !... You rocks
Good luck! Let me know if it works - if you have the time to answer.
We are working on a coarse-grained approach that could be useful for membranes.
It is very difficult to compromise (CPU time/ versus satisfactory results).
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