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user366312
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9 votes
1 answer
340 views

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

7 votes
2 answers
410 views

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

6 votes
1 answer
94 views

How are tertiary protein structures represented in computers?

6 votes
1 answer
833 views

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

6 votes
1 answer
102 views

Does Bioinformatics have any relationship with protein modeling and simulation?

6 votes
3 answers
2k views

What programming language do matter modelers generally use?

6 votes
1 answer
128 views

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

6 votes
3 answers
1k views

Which MD software is preferable for protein simulation?

5 votes
1 answer
152 views

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

5 votes
1 answer
68 views

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

5 votes
2 answers
312 views

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

5 votes
1 answer
100 views

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

5 votes
2 answers
283 views

Scales for simulation

5 votes
1 answer
237 views

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

5 votes
3 answers
312 views

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

4 votes
2 answers
179 views

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

4 votes
2 answers
159 views

What is a "transient" state?

4 votes
1 answer
309 views

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

4 votes
1 answer
139 views

Understanding use of Machine Learning in Multiscale Enhanced Sampling

4 votes
1 answer
159 views

Why is this source code giving incorrect RMSD value?

4 votes
0 answers
71 views

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

4 votes
0 answers
76 views

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

4 votes
0 answers
62 views

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

4 votes
1 answer
159 views

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

4 votes
1 answer
141 views

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

4 votes
1 answer
358 views

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

4 votes
1 answer
40 views

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

4 votes
2 answers
353 views

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

4 votes
2 answers
240 views

Thermodynamics: System versus Ensemble

3 votes
1 answer
53 views

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