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user366312
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6 votes
3 answers
2k views

What programming language do matter modelers generally use?

6 votes
3 answers
791 views

Which MD software is preferable for protein simulation?

6 votes
1 answer
787 views

What is the fundamental difference between the Ising and Potts models?

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"?

2 votes
1 answer
602 views

Why do we even need periodic boundary conditions?

3 votes
2 answers
494 views

Why should the concept of "nearest/minimum/closest image" even come into the discussion of molecular simulation?

3 votes
1 answer
403 views

Where can I find this formula?

7 votes
2 answers
394 views

What does it mean by "transferable" in the case of a force field?

4 votes
1 answer
345 views

What is the procedure to develop a new force field for molecular simulation?

9 votes
1 answer
323 views

Difference between Statistical Physics, Statistical Mechanics, and Molecular Modeling?

4 votes
2 answers
313 views

What is the difference between a "periodic image" and a "nearest image" in MD simulation?

5 votes
3 answers
310 views

Are MD and MC both able to study both equilibrium and non-equilibrium systems?

4 votes
1 answer
288 views

How can I identify phase transition from a plot of Ising model?

5 votes
2 answers
283 views

Scales for simulation

2 votes
1 answer
251 views

What are some ways to check if a molecular simulation is running properly?

5 votes
2 answers
246 views

Do "minimum image convention" and "nearest image" talks about the same things?

4 votes
2 answers
235 views

Thermodynamics: System versus Ensemble

5 votes
1 answer
221 views

Where can I find the source code from the book "The Art of Molecular Dynamics Simulation"?

2 votes
1 answer
207 views

From a PDB file, how may I know which atoms have bonds between them?

4 votes
2 answers
176 views

What does it mean by "scale mismatch" and "bridging of scales"?

2 votes
1 answer
172 views

What are some symptoms that could tell me that my simulation is not running properly?

3 votes
2 answers
167 views

What is the relationship between periodic boundary and the simulation box?

4 votes
2 answers
156 views

What is a "transient" state?

4 votes
1 answer
155 views

Definition of the terms "modeling" and "simulation" in the context of biomolecules and/or proteins

4 votes
1 answer
153 views

Why is this source code giving incorrect RMSD value?

4 votes
1 answer
138 views

Understanding use of Machine Learning in Multiscale Enhanced Sampling

3 votes
1 answer
137 views

When should I use Charge-Charge Interactions, Charge-Dipole Interactions, and Dipole-Dipole Interactions in molecular simulation?

2 votes
2 answers
136 views

What is the minimum number of atoms required to run a Monte Carlo simulation meaningfully?

4 votes
1 answer
136 views

What does it mean by a "restraint" in the case of a protein chain?

3 votes
0 answers
130 views

Molecular MC simulation is not equilibrating [closed]