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user366312
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5 votes
1 answer
53 views

Does GROMACS have the capability to do Monte Carlo simulation of proteins?

2 votes
0 answers
30 views

How can I determine if a system is equilibrated?

3 votes
0 answers
30 views

How can I compute the longest relaxation time?

2 votes
0 answers
51 views

How do I validate and benchmark a new protein or polymer model?

6 votes
3 answers
791 views

Which MD software is preferable for protein simulation?

5 votes
1 answer
122 views

Plot MSD (mean square displacement) versus time for a polymer chain

5 votes
1 answer
100 views

Why do we need to find minimum energy in a protein chain?

3 votes
1 answer
53 views

What is a 'mover' in molecular dynamics?

2 votes
0 answers
59 views

Method for Energy Computation of Protein Structures

-4 votes
1 answer
101 views

Are these simulator, visualizer, or force field? [closed]

2 votes
1 answer
207 views

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

4 votes
1 answer
138 views

Understanding use of Machine Learning in Multiscale Enhanced Sampling

1 vote
0 answers
62 views

Where should we compute `Energy` in this listing? [closed]

2 votes
0 answers
46 views

Where should we compute `Trajectory` in this listing?

3 votes
1 answer
52 views

Is the following description talking about the simulation box or the boundary condition?

2 votes
1 answer
29 views

Why do I see a deviation when I compare PDBs using TMalign?

4 votes
2 answers
235 views

Thermodynamics: System versus Ensemble

3 votes
1 answer
137 views

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

6 votes
1 answer
124 views

Is the term "Forcefield" only reserved for MD (Molecular Dynamics)?

2 votes
0 answers
66 views

Are lattice-based Monte Carlo simulations used in the case of liquids and gases?

6 votes
3 answers
2k views

What programming language do matter modelers generally use?

2 votes
0 answers
43 views

What factors determine the selection of a specific type of MC move?

2 votes
2 answers
136 views

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

5 votes
2 answers
246 views

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

4 votes
2 answers
313 views

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

3 votes
2 answers
494 views

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

2 votes
1 answer
251 views

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

2 votes
1 answer
172 views

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

4 votes
1 answer
345 views

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

5 votes
3 answers
310 views

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