User user366312

8 votes

1 answer

273 views

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

asked Apr 29 at 21:20

7 votes

2 answers

353 views

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

asked May 21, 2022 at 20:21

6 votes

1 answer

89 views

How are tertiary protein structures represented in computers?

asked Jul 20, 2021 at 9:44

6 votes

1 answer

672 views

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

asked Sep 17, 2022 at 8:59

6 votes

1 answer

86 views

Does Bioinformatics have any relationship with protein modeling and simulation?

asked Mar 4 at 9:21

6 votes

3 answers

2k views

What programming language do matter modelers generally use?

asked Jun 18 at 11:36

6 votes

1 answer

119 views

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

asked Jun 22 at 18:35

5 votes

2 answers

137 views

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

asked Jun 10 at 18:26

5 votes

1 answer

59 views

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

asked Nov 18 at 16:40

5 votes

1 answer

95 views

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

asked Oct 20, 2022 at 12:43

5 votes

2 answers

280 views

Scales for simulation

asked Jul 4, 2022 at 11:19

5 votes

1 answer

174 views

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

asked May 22 at 18:25

5 votes

3 answers

303 views

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

asked May 26 at 19:17

4 votes

2 answers

168 views

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

asked Jul 17, 2022 at 15:27

4 votes

2 answers

149 views

What is a "transient" state?

asked Sep 15, 2022 at 4:31

4 votes

1 answer

256 views

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

asked Jan 27 at 16:06

4 votes

1 answer

135 views

Understanding use of Machine Learning in Multiscale Enhanced Sampling

asked Jun 16, 2022 at 18:08

4 votes

1 answer

133 views

Why is this source code giving incorrect RMSD value?

asked Oct 21, 2022 at 10:46

4 votes

0 answers

71 views

Can you recommend a molecular modeling book targeted at polymers or biomolecules that supplies programming examples? [closed]

asked Apr 17, 2022 at 18:53

4 votes

0 answers

68 views

What does it mean by pruning and enrichment in the case of Rosenbluth method? [closed]

asked Apr 23, 2022 at 19:14

4 votes

0 answers

61 views

Where should I apply the harmonic spring function in the case of polymer simulation? [closed]

asked Apr 24, 2022 at 17:39

4 votes

1 answer

146 views

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

asked May 22, 2022 at 12:09

4 votes

1 answer

358 views

Which MD software is preferable for protein simulation?

asked Oct 5 at 2:04

4 votes

1 answer

115 views

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

asked Apr 20 at 14:17

4 votes

1 answer

315 views

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

asked Jun 2 at 23:56

4 votes

1 answer

39 views

Can you supply me with some book names on MC protein simulation?

asked Apr 28 at 2:34

4 votes

2 answers

228 views

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

asked Jun 10 at 16:12

4 votes

2 answers

222 views

Thermodynamics: System versus Ensemble

asked Jul 2 at 4:34

3 votes

1 answer

50 views

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

asked Sep 5 at 8:44

3 votes

1 answer

127 views

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

asked Jun 24 at 5:27

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63 Questions

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

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

How are tertiary protein structures represented in computers?

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

Does Bioinformatics have any relationship with protein modeling and simulation?

What programming language do matter modelers generally use?

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

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

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

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

Scales for simulation

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

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

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

What is a "transient" state?

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

Understanding use of Machine Learning in Multiscale Enhanced Sampling

Why is this source code giving incorrect RMSD value?

Can you recommend a molecular modeling book targeted at polymers or biomolecules that supplies programming examples? [closed]

What does it mean by pruning and enrichment in the case of Rosenbluth method? [closed]

Where should I apply the harmonic spring function in the case of polymer simulation? [closed]

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

Which MD software is preferable for protein simulation?

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

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

Can you supply me with some book names on MC protein simulation?

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

Thermodynamics: System versus Ensemble

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

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