Software News and Update Reconstruction of Atomistic Details from Coarse-Grained Structures
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Citations
Going Backward : A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models
The power of coarse graining in biomolecular simulations
Computational Modeling of Realistic Cell Membranes
Probing the Self-Assembly Mechanism of Diphenylalanine-Based Peptide Nanovesicles and Nanotubes
Classical electrostatics for biomolecular simulations.
References
Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature.
A generalized reaction field method for molecular dynamics simulations
The GROMOS96 Manual and User Guide
A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field
Coarse-Graining of Condensed Phase and Biomolecular Systems
Related Papers (5)
Frequently Asked Questions (16)
Q2. Why are the AA particles randomly placed around the corresponding CG beads?
Because the AA particles are initially placed randomly around the corresponding CG beads, very large forces will occur at the beginning of the simulation and cause numerical instabilities.
Q3. Why is the annealing used to optimize low-energy structures?
because the annealing is merely used to optimize low-energy structures, and not to calculate dynamic properties of the system, the mass of the hydrogen atoms can be increased, which would allow for a larger integration time step.
Q4. How many nanoseconds can be used to simulate a molecule?
The huge computational effort involved in conventional atomistic MD simulations currently limits accessible simulation times to hundreds of nanoseconds and length scales to tens of nanometers.
Q5. What is the probability of a structure with both stereocenters inverted?
In about 8% of the cases, a structure was obtained in which one of the two stereocenters is inverted, whereas a structure with both stereocenters inverted occurred at a probability of only 2%.
Q6. Why is the methyl group bound to C10 on the wrong side of the plane?
Because of the random initial placement of the atoms close to their reference CG beads (see Methods), there is a chance that, e.g., the methyl group bound to C10 is initially on the “wrong” side of the plane spanned by the other three bound groups.
Q7. What are the distributions obtained with the 2- to-1 mapping?
The distributions obtained with the 2- to-1 (dashed red curve) and 1-to-1 mapping (solid red curve) have even lower average energies and are very sharp.
Q8. What was the first step in the reconstruction of a CG system?
a system composed of the WALP20 transmembrane peptide embedded in a solvated DPPC bilayer was reconstructed from its CG representation.
Q9. How was the reconstruction of a WALP20 peptide performed?
To generate a starting structure for the subsequent reconstruction simulations, a 40-ns CG simulation (MARTINI force field) of a system containing a WALP20 peptide embedded in a membrane bilayer composed of 112 DPPC lipids, solvated by 1186 water beads, was carried out at T = 323 K in the NPT ensemble (p = 1 bar).
Q10. What are the properties of the ensemble of reconstructed atomistic structures?
the authors investigated how the properties of the ensemble of reconstructed atomistic structures depend on two crucial parameters of the SA: the total annealing time, ttot , and the initial temperature, Tinit .
Q11. What is the atomistic representation of a WALP20 peptide?
a system composed of a WALP20 transmembrane peptide embedded in a solvated DPPC bilayer was transformed from a CG to an atomistic representation.
Q12. What is the main method used to optimize low-energy ensembles?
A three-step approach is used to optimize low-energy ensembles: First, the atomistic particles are positioned close to their reference CG beads.
Q13. What is the purpose of the reconstruction method?
By this means, the reconstruction method allows to check and validate the results and predictions obtained with CG models against atomistic models, thereby combining the efficiency of the former with the accuracy of the latter.
Q14. How long is the simulation required to obtain a low-energy structure?
Although the helical structure of the peptide is already fullyformed in about 20 ps, the potential energy of the system (dashed line in Fig. 9) indicates that also in this case, simulation times longer than about 60 ps are required to obtain a low-energy structure.
Q15. What mapping scheme was used to map the dihedral angle of asparagine?
The different mapping schemesapplied were an amino acid-to-1 mapping, i.e., each CG bead represents a complete amino acid; the MARTINI mapping, in which on an average four heavy atoms are mapped onto one CG bead; and a 2-to-1 mapping, i.e., each CG bead represents two heavy atoms.
Q16. What was the first set of reconstruction simulations?
The second set of reconstruction simulations (Set2) started from a snapshot taken from an equilibrium MARTINI CG simulation at 300 K.