Questions tagged [martini]
Questions about the Martini forcefield and related programs such as MartiniTools, Martinize, Martinize2, etc.
7
questions
3
votes
0
answers
28
views
martinize issue
PS C:\Users\MALINE\Desktop\martini> python martinize.py -f polypropylene.pdb -o output.pdb
...
1
vote
1
answer
143
views
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:
...
- 3,145
2
votes
1
answer
60
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....
- 24k
2
votes
0
answers
48
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 ...
- 4,406
6
votes
0
answers
103
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....
- 1,404
9
votes
1
answer
831
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 ...
- 15.7k
6
votes
0
answers
845
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 ...