|
Deform by Gromacs to apply shear rate
|
|
8
|
2562
|
June 9, 2026
|
|
COM motion removal during NVT simulation with electric field
|
|
5
|
81
|
May 19, 2026
|
|
Mdrun with awh for a dimeric protein
|
|
0
|
37
|
April 29, 2026
|
|
GROMACS SMD for TCR–pMHC: should TCR be pull group 1 or 2
|
|
0
|
33
|
April 25, 2026
|
|
Using AWH for bilayer permeability
|
|
18
|
1354
|
April 22, 2026
|
|
Changes of default `nstpcouple` and `nsttcouple` from version 2022 to 2023
|
|
35
|
2430
|
April 14, 2026
|
|
C-rescale vs Parrinello–Rahman in final NPT equilibration before protein–protein SMD (TCR–pMHC, ~1M
|
|
1
|
114
|
April 8, 2026
|
|
Abnormal dVremain/dl values in GROMACS 2025.0 with vdw-type=pme and free-energy
|
|
3
|
21
|
March 31, 2026
|
|
Coulomb (SR) calculation in PME
|
|
9
|
81
|
March 19, 2026
|
|
Steered Molecular dynamics of a ligand moving towards bilayer membrane
|
|
1
|
57
|
March 16, 2026
|
|
Paradoxical Density in OPLS-AA: Diesel mixture density is abnormally LOWER than its lightest compone
|
|
6
|
56
|
March 15, 2026
|
|
Hydrogen mass repartitioning + multiple time step
|
|
2
|
48
|
March 7, 2026
|
|
ERROR 1 rvdw-switch must be < rvdw INQUIRY?
|
|
4
|
45
|
March 5, 2026
|
|
Steered MD Simulation error
|
|
19
|
194
|
February 19, 2026
|
|
Discrete "Coulp.-recip" values for different conformations of the same system
|
|
10
|
80
|
February 18, 2026
|
|
Equilibration not work
|
|
0
|
28
|
February 17, 2026
|
|
SMD simulation - protein pulling and resulting rotation
|
|
2
|
82
|
February 10, 2026
|
|
Questions regarding AWH and comparison to MBAR
|
|
3
|
105
|
February 10, 2026
|
|
[Errors] Problems during Umbrella Sampling
|
|
1
|
53
|
February 4, 2026
|
|
Your Review on AMBER19sb MD in GROMACS2026
|
|
1
|
164
|
February 4, 2026
|
|
The contradiction between the mdp settings and the real pull rate
|
|
13
|
104
|
February 4, 2026
|
|
Simulated annealing of protein-DNA complex
|
|
0
|
64
|
February 3, 2026
|
|
Free energy verification by thermodynamic integration in liquid solutions
|
|
0
|
43
|
January 22, 2026
|
|
Tabulated nonbonded potentials in GROMACS 2026
|
|
1
|
68
|
January 21, 2026
|
|
Comparing Simulations with Different Thermo/Barostats
|
|
2
|
70
|
January 21, 2026
|
|
Water box elongation
|
|
1
|
35
|
January 21, 2026
|
|
Conducting MD simulation on a zinc metalloprotein with 4 zinc ions
|
|
0
|
62
|
January 7, 2026
|
|
Steered MD Simulation using Gromacs
|
|
2
|
97
|
January 7, 2026
|
|
High pressure in x and y axis in a buble in a nano channel
|
|
2
|
43
|
January 5, 2026
|
|
Steered molecular dynamics - umbrella samling
|
|
1
|
87
|
December 8, 2025
|