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C-rescale barostat and simulated annealing
|
|
4
|
31
|
August 6, 2026
|
|
Z‑dimension of the box decreases
|
|
3
|
43
|
August 5, 2026
|
|
PBC Box Failing to Expand to Input .gro File Parameters + Unwanted Position Restrained Protein
|
|
2
|
53
|
July 30, 2026
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|
Trans to cis confirmation at NVT step
|
|
0
|
25
|
July 28, 2026
|
|
How many nanoseconds do I need to capture potential unbinding events for protein-protein interaction
|
|
1
|
57
|
July 4, 2026
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Deform by Gromacs to apply shear rate
|
|
8
|
2605
|
June 9, 2026
|
|
COM motion removal during NVT simulation with electric field
|
|
5
|
93
|
May 19, 2026
|
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Mdrun with awh for a dimeric protein
|
|
0
|
40
|
April 29, 2026
|
|
GROMACS SMD for TCR–pMHC: should TCR be pull group 1 or 2
|
|
0
|
38
|
April 25, 2026
|
|
Using AWH for bilayer permeability
|
|
18
|
1414
|
April 22, 2026
|
|
Changes of default `nstpcouple` and `nsttcouple` from version 2022 to 2023
|
|
35
|
2501
|
April 14, 2026
|
|
C-rescale vs Parrinello–Rahman in final NPT equilibration before protein–protein SMD (TCR–pMHC, ~1M
|
|
1
|
168
|
April 8, 2026
|
|
Abnormal dVremain/dl values in GROMACS 2025.0 with vdw-type=pme and free-energy
|
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3
|
31
|
March 31, 2026
|
|
Coulomb (SR) calculation in PME
|
|
9
|
107
|
March 19, 2026
|
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Steered Molecular dynamics of a ligand moving towards bilayer membrane
|
|
1
|
68
|
March 16, 2026
|
|
Paradoxical Density in OPLS-AA: Diesel mixture density is abnormally LOWER than its lightest compone
|
|
6
|
69
|
March 15, 2026
|
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Hydrogen mass repartitioning + multiple time step
|
|
2
|
61
|
March 7, 2026
|
|
ERROR 1 rvdw-switch must be < rvdw INQUIRY?
|
|
4
|
57
|
March 5, 2026
|
|
Steered MD Simulation error
|
|
19
|
298
|
February 19, 2026
|
|
Discrete "Coulp.-recip" values for different conformations of the same system
|
|
10
|
97
|
February 18, 2026
|
|
Equilibration not work
|
|
0
|
35
|
February 17, 2026
|
|
SMD simulation - protein pulling and resulting rotation
|
|
2
|
103
|
February 10, 2026
|
|
Questions regarding AWH and comparison to MBAR
|
|
3
|
119
|
February 10, 2026
|
|
[Errors] Problems during Umbrella Sampling
|
|
1
|
61
|
February 4, 2026
|
|
Your Review on AMBER19sb MD in GROMACS2026
|
|
1
|
196
|
February 4, 2026
|
|
The contradiction between the mdp settings and the real pull rate
|
|
13
|
125
|
February 4, 2026
|
|
Simulated annealing of protein-DNA complex
|
|
0
|
94
|
February 3, 2026
|
|
Free energy verification by thermodynamic integration in liquid solutions
|
|
0
|
54
|
January 22, 2026
|
|
Tabulated nonbonded potentials in GROMACS 2026
|
|
1
|
90
|
January 21, 2026
|
|
Comparing Simulations with Different Thermo/Barostats
|
|
2
|
110
|
January 21, 2026
|