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Questions tagged [coarse-grained]

For models of molecular/biomolecular systems that reduce complexity by using a simplified representation of groups of atoms. One common example is the Martini force field

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Protein structure prediction: levels of coarse-graining in deep learning approaches

I am researching the areas of protein structure prediction, protein + ligand pose prediction, and co-folding algos with deep learning. I am trying to map the current state of the art architectures ...
operator's user avatar
1 vote
1 answer
84 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: ...
Pranoy Ray's user avatar
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4 votes
1 answer
87 views

To what extent can coarse-grained models retain the essential quantum mechanical characteristics of a system?

To what extent can current coarse-grained models, within the context of multiscale modelling, retain essential quantum mechanical characteristics such as electron correlation, polarization, and ...
Magic_Number's user avatar
4 votes
1 answer
139 views

Understanding use of Machine Learning in Multiscale Enhanced Sampling

Multiscale Enhanced Sampling Using Machine Learning Multiscale enhanced sampling (MSES) allows for enhanced sampling of all-atom protein structures by coupling with the accelerated dynamics of the ...
user366312's user avatar
  • 2,546
3 votes
3 answers
682 views

Is it correct to say "in molecular dynamics we are faced with..." or should it be "in molecular modeling we are faced with"?

In the paper "DeePCG: Constructing coarse-grained models via deep neural networks", it says: "In molecular dynamics (MD), we are often faced with two types of coarse-graining tasks. In ...
user366312's user avatar
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8 votes
0 answers
205 views

Young's modulus from MD simulation [closed]

I have a coarse-grained model of a surface which is almost planar/flat in 2D. Now, I want to compute some of its mechanical properties to test it. Young's modulus is one of the properties that come to ...
Roshan Shrestha's user avatar
4 votes
0 answers
65 views

Using DPD/LAMMPS how does a protein remains a protein although there are no attractive forces in DPD? [closed]

I am new to LAMMPS/DPD (Dissipative particle dynamics), but as i read through DPD model there are three main forces between beads (beads are the spheres consisting of a group of atoms). FC which is a ...
Delaram Nematollahi's user avatar
5 votes
0 answers
123 views

How to define a simple potential in DPD for some type of beads? [closed]

I apologize if this is off-topic and if so would be grateful for someone to point me to a relevant source of information. Dissipative Particle Dynamics (DPD) is a quick simulation technique that ...
Delaram Nematollahi's user avatar
12 votes
2 answers
458 views

What kind of systems do we need to coarse-grain to observe interesting phenomena?

When I go to talks, I hear the statement "coarse-graining is required to access spatio-temporal scales to observe important dynamical behavior for stimuli-responsive systems" before they go ...
megamence's user avatar
  • 4,171
6 votes
0 answers
739 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 ...
Vranvs's user avatar
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9 votes
1 answer
755 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 ...
Vranvs's user avatar
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10 votes
2 answers
962 views

How can I modify the Martini v2 or v3 force field to increase the Lennard Jones potential well depth (epsilon)?

I am trying to run some coarse-grained simulations of an Intrinsically Disordered Protein (IDP) using the Martini force field, and I want to increase the strength of interaction between water and ...
Vranvs's user avatar
  • 423
10 votes
1 answer
149 views

Understanding the rigorous bridge between atomistic and coarse-grained simulations

I am currently reading this paper by Noid et. al. on the rigorous bridge between atomistic and coarse-grained simulations. In the paper, he defined a linear map from the atomistic coordinates and ...
megamence's user avatar
  • 4,171