|
What is the proper way of doing Free energy calculations in gromacs?
|
|
2
|
62
|
February 4, 2025
|
|
Expanded ensemble: Performance impact of perturbing more atoms
|
|
4
|
24
|
January 23, 2025
|
|
Free energy of mutation - example on an amino acid
|
|
0
|
41
|
January 6, 2025
|
|
Analysis of AWH simulations
|
|
2
|
56
|
November 18, 2024
|
|
Cutoff-dependent deviations in free energy for force switching and potential shifting
|
|
3
|
62
|
October 23, 2024
|
|
Applying restraining for a ligand in a binding pocket in ABFE calculation
|
|
1
|
23
|
October 18, 2024
|
|
Free energy, annihilation: charged ligand
|
|
7
|
99
|
October 17, 2024
|
|
Is gmx bar reading dH/dl for masses?
|
|
8
|
64
|
October 15, 2024
|
|
Restraints free energy
|
|
1
|
71
|
September 21, 2024
|
|
Free energy annihilation chromophore in scaffold
|
|
6
|
37
|
September 20, 2024
|
|
MDP files for DNA free energy perturbation (equilibrium)
|
|
0
|
21
|
September 18, 2024
|
|
Mutating residue, free energy
|
|
3
|
94
|
September 18, 2024
|
|
Fatal error: Perturbed masses or constraints are not supported by rerun
|
|
1
|
34
|
September 10, 2024
|
|
Charged solute, thermodynamic integration, couple-intramol = yes
|
|
0
|
49
|
September 1, 2024
|
|
Gmx bar output - central limit theorem
|
|
0
|
42
|
August 30, 2024
|
|
Gmx bar output: interpretation of +/- error estimations
|
|
0
|
40
|
August 30, 2024
|
|
PMF of interaction between a positive ion and a negative ion
|
|
0
|
19
|
August 27, 2024
|
|
Pull code for a single window
|
|
3
|
22
|
August 22, 2024
|
|
Ligand binding free energy in a burried pocket
|
|
8
|
138
|
August 21, 2024
|
|
Gaussian quadrature in thermodynamic integration
|
|
0
|
35
|
August 20, 2024
|
|
Solvation free energy calculation
|
|
2
|
89
|
August 13, 2024
|
|
Free energy calculation with fixed relative position
|
|
2
|
49
|
August 12, 2024
|
|
TI - Free Energy - couple-intramol=no
|
|
35
|
2534
|
August 6, 2024
|
|
How to decouple the Lennard-Jones (LJ) interaction between two particular atoms in a same molecule?
|
|
0
|
29
|
July 11, 2024
|
|
Problems in PMF curve of AquaporinZ after umbrella sampling
|
|
18
|
381
|
July 1, 2024
|
|
Incorrect relative solvation free energy values using single topology alchemical transformation
|
|
8
|
327
|
May 5, 2024
|
|
Simulations with free energy calculations on GPU is several time slower than normal simulations
|
|
6
|
1011
|
April 26, 2024
|
|
Why is coulomb SR energy different sign using different forcefields?
|
|
13
|
542
|
April 11, 2024
|
|
Dummy Alchemical Ions in Gromacs
|
|
0
|
222
|
April 2, 2024
|
|
MMPBSA value is a possitive
|
|
4
|
284
|
April 2, 2024
|