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 ...
- 15.7k
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 ...
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 ...
- 1,404
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 ...
- 15.7k
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, ...
- 24k
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..."...
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 ...
- 41
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 ...
- 2,962
2
votes
Accepted
Choosing Between a Small Cluster and a Workstation for MD Simulations and Quantum Chemistry Calculations
Go for gaming PCs. Especially if you are using GROMACS. You'll get significantly
more performance out of RTX40NN GPUs and 13th/14th gen. Intel i7s than you will out of pre-built workstations,
and you ...
- 421
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 ...
- 3,145
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 ...
Only top scored, non community-wiki answers of a minimum length are eligible