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Mdp file differences between CHARMM27 and CHARMM36 parameters
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4
|
47
|
October 7, 2026
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PBC Box Failing to Expand to Input .gro File Parameters + Unwanted Position Restrained Protein
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3
|
91
|
September 2, 2026
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NPγT vs NPT for Unrestrained Membrane Equilibration Using the CHARMM36 Force Field
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10
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186
|
August 26, 2026
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CUDA illegal memory access during NPT equilibration
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9
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131
|
August 21, 2026
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C-rescale barostat and simulated annealing
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4
|
97
|
August 6, 2026
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Z‑dimension of the box decreases
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3
|
86
|
August 5, 2026
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Trans to cis confirmation at NVT step
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0
|
33
|
July 28, 2026
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How many nanoseconds do I need to capture potential unbinding events for protein-protein interaction
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1
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86
|
July 4, 2026
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Deform by Gromacs to apply shear rate
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8
|
2661
|
June 9, 2026
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COM motion removal during NVT simulation with electric field
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5
|
140
|
May 19, 2026
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Mdrun with awh for a dimeric protein
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0
|
52
|
April 29, 2026
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GROMACS SMD for TCR–pMHC: should TCR be pull group 1 or 2
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0
|
51
|
April 25, 2026
|
|
Using AWH for bilayer permeability
|
|
18
|
1481
|
April 22, 2026
|
|
Changes of default `nstpcouple` and `nsttcouple` from version 2022 to 2023
|
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35
|
2697
|
April 14, 2026
|
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C-rescale vs Parrinello–Rahman in final NPT equilibration before protein–protein SMD (TCR–pMHC, ~1M
|
|
1
|
224
|
April 8, 2026
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Abnormal dVremain/dl values in GROMACS 2025.0 with vdw-type=pme and free-energy
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3
|
46
|
March 31, 2026
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Coulomb (SR) calculation in PME
|
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9
|
137
|
March 19, 2026
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Steered Molecular dynamics of a ligand moving towards bilayer membrane
|
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1
|
85
|
March 16, 2026
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Paradoxical Density in OPLS-AA: Diesel mixture density is abnormally LOWER than its lightest compone
|
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6
|
101
|
March 15, 2026
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Hydrogen mass repartitioning + multiple time step
|
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2
|
93
|
March 7, 2026
|
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ERROR 1 rvdw-switch must be < rvdw INQUIRY?
|
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4
|
86
|
March 5, 2026
|
|
Steered MD Simulation error
|
|
19
|
346
|
February 19, 2026
|
|
Discrete "Coulp.-recip" values for different conformations of the same system
|
|
10
|
119
|
February 18, 2026
|
|
Equilibration not work
|
|
0
|
37
|
February 17, 2026
|
|
SMD simulation - protein pulling and resulting rotation
|
|
2
|
124
|
February 10, 2026
|
|
Questions regarding AWH and comparison to MBAR
|
|
3
|
148
|
February 10, 2026
|
|
[Errors] Problems during Umbrella Sampling
|
|
1
|
76
|
February 4, 2026
|
|
Your Review on AMBER19sb MD in GROMACS2026
|
|
1
|
234
|
February 4, 2026
|
|
The contradiction between the mdp settings and the real pull rate
|
|
13
|
191
|
February 4, 2026
|
|
Simulated annealing of protein-DNA complex
|
|
0
|
117
|
February 3, 2026
|