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fireball.1
  • Member for 3 years, 11 months
  • Last seen more than a month ago
4 votes
0 answers
65 views

Gromacs generate forces using .pdb topol.top and .mdp file [closed]

7 votes
1 answer
637 views

Gromacs generate charges for a .pdb file

6 votes
0 answers
140 views

How to calculate and plot the electrostatic forces in a .pdb file [closed]

7 votes
1 answer
3k views

How to generate a .tpr file from a .pdb or .xyz file in gromacs

8 votes
2 answers
499 views

File type to write bond information

11 votes
2 answers
2k views

How to include individual PBC box dimensions in xyz file format compatible with VMD

11 votes
2 answers
2k views

Recalculate atom positions to account for periodic boundary conditions

8 votes
1 answer
99 views

What software can perform block analysis on time sequence data?

7 votes
0 answers
229 views

Collective variable to determine the number of bonds in the shortest Hydrogen bond wire [closed]

10 votes
1 answer
252 views

Can I compute the free energy difference in (temporally) nearby micro-states using the Zwanzig equation for Free Energy Perturbation?

7 votes
1 answer
143 views

Does the Hamiltonian of an unbiased simulation change when the simulation moves from a stable basin to another?

11 votes
0 answers
251 views

Calculate free energy for a canonical (NVT) ensemble [closed]