Questions tagged [martini]
Questions about the Martini forcefield and related programs such as MartiniTools, Martinize, Martinize2, etc.
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How can I use ss2 or FASTA files as inputs for protein-folding simulation using the MARTINI course-grained model?
I asked this at Biostars but the post seems to have been deleted there.
My professor told me to implement MARTINI ForceField-based coarse-grained model to simulate 2GB1A protein-folding using Python-3....
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Martini 3 CG water cluster is not becoming spherical under NVT conditions [closed]
When we put a certain number of molecules in a small cubic box, and put it inside a large cubic box, under NVT simulation, the water cubic box is supposed to be spherical in shape to reach a minimum ...
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Calculating bending modulus of a CG model of a surface from MD simulation
I have built a CG (Martini) model of a 2D Nanomaterial. For now, I want to calculate its bending rigidity. As far as I know, the bending modulus can be computed by making the nanomaterial infinite - i....
- 1,066
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Back-mapping Martini 3 coarse-grain to all-atom representations [closed]
I have a $10\mu s$ trajectory with 10,000 frames that I would like to backmap to atomistic representations so that I can compare my ensemble to experimental measurements.
I am using MartiniTools for ...
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answer
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What is the purpose of DSSP when using martinize2?
I am studying an IDP with a lot of helical secondary structure, and trying to find a trajectory that I can use as an ensemble that fits my SAXS data. My starting models are the output from the Robetta ...
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