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3 votes
1 answer
137 views

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

3 votes
1 answer
52 views

What is a 'mover' in molecular dynamics?

3 votes
2 answers
493 views

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

3 votes
0 answers
30 views

How can I compute the longest relaxation time?

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"?

3 votes
2 answers
167 views

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

3 votes
0 answers
84 views

What are the similarities between MD and MC in the case of protein simulation? [closed]

3 votes
1 answer
403 views

Where can I find this formula?

3 votes
1 answer
73 views

What formula should I use to calculate the total energy of a linear polymer chain?

3 votes
0 answers
130 views

Molecular MC simulation is not equilibrating [closed]

3 votes
1 answer
61 views

How should I calculate total potential in a polymer chain?

3 votes
1 answer
127 views

Are MD and MC both parts of statistical physics?

2 votes
1 answer
29 views

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

2 votes
0 answers
45 views

How can I compute the performance of an application software? [closed]

2 votes
1 answer
56 views

How can I use ss2 or FASTA files as inputs for protein-folding simulation using the MARTINI course-grained model?

2 votes
0 answers
58 views

How can I calculate the radius of a residue? [closed]

2 votes
1 answer
597 views

Why do we even need periodic boundary conditions?

2 votes
1 answer
104 views

What do we simulate with molecular simulation of proteins in the theoretical research?

2 votes
1 answer
54 views

What does it mean by a "site" in the case of a CG model?

2 votes
0 answers
47 views

Can protein modeling and simulation be used in developing a marketable product? [closed]

2 votes
0 answers
30 views

How can I determine if a system is equilibrated?

2 votes
0 answers
51 views

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

2 votes
1 answer
194 views

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

2 votes
0 answers
59 views

Method for Energy Computation of Protein Structures

2 votes
2 answers
136 views

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

2 votes
0 answers
43 views

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

2 votes
0 answers
66 views

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

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?

2 votes
0 answers
46 views

Where should we compute `Trajectory` in this listing?