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10 votes
Accepted

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

Since you seem to have at least a start on automating the process of modifying the file, I will just address the other two parts of your question: the format of the ...
Tyberius's user avatar
  • 15.5k
8 votes
Accepted

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

"What kind of systems do we need to coarse-grain to observe interesting phenomena?" Systems that would otherwise be too large and/or complicated to simulate in a reasonable amount of time ...
Nike Dattani - No Free Time's user avatar
7 votes

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

Generally, in multi-scale modelling, QM characteristics are irrelevant. Most of the processes that we study for these multi-scale modelling are thermodynamics driven. So, I will be very surprised if ...
Roshan Shrestha's user avatar
7 votes

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

I believe I have figured it out. For those trying to martinize their all-atom files into coarse grain representations for martini 3, use the following package: https://github.com/marrink-lab/vermouth-...
Vranvs's user avatar
  • 423
6 votes
Accepted

Understanding the rigorous bridge between atomistic and coarse-grained simulations

Before working through the equations, I'll try to explain the logic behind what they are doing. It helps to think of think of their process backwards and assume they want an expression like equation ...
Tyberius's user avatar
  • 15.5k
6 votes

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

The answer given by @NikeDattani is very complete. My two cents... As the systems get bigger and bigger and the computational resources, even with the GPU development, doesn't grow in the same speed, ...
Camps's user avatar
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5 votes

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

From a grammatical perspective, I agree with you. It would have been better for them to have said "in molecular dynamics calculations...". instead of just "in molecular dynamics..."...
Nike Dattani - No Free Time's user avatar
4 votes

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

I disagree. Generally the term "molecular dynamics" (MD) is used of a particular kind of simulation, to wit the kind where you model the forces that act on atoms and then calculate their ...
QuantumWiz's user avatar
4 votes
Accepted

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

Technically, I think you are correct: if you are talking about both molecular dynamics simulations and Monte Carlo methods, then you are talking about molecular modelling. But why not get even more ...
Shern Ren Tee's user avatar
1 vote

How to use martinize.py?

As per the README we can invoke martinize as follows: martinize.py -i input.pdb -o output.pdb I ran the command on a PDB of 4poj And I get the following output ...
Vandan Revanur's user avatar
1 vote

Understanding use of Machine Learning in Multiscale Enhanced Sampling

Since this is not an active problem for the researcher anymore, I'm removing it from the unanswered queue, but if anyone wants to write another answer, please just comment here and I will remove this ...
1 vote
Accepted

What is the purpose of DSSP when using martinize2?

Just basically collecting the comments here. The tutorials page for Martini states: The secondary structure of the protein influences both the selected bead types and bond/angle/dihedral parameters ...

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