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 ...
  • 14.3k
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 ...
  • 29.2k
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-...
  • 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 ...
  • 14.3k
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, ...
  • 19.3k
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..."...
  • 29.2k
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 ...
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 ...
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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