Questions tagged [martini]

Questions about the Martini forcefield and related programs such as MartiniTools, Martinize, Martinize2, etc.

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1 answer
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How to use martinize.py?

I have been trying to get the CG representation of a basic octane molecule. The pdb file is as follows: ...
2 votes
1 answer
54 views

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....
2 votes
0 answers
47 views

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 ...
6 votes
0 answers
101 views

Calculating bending modulus of a CG model of a surface from MD simulation [closed]

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....
9 votes
1 answer
707 views

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 ...
6 votes
0 answers
656 views

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 ...