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Position restraints and mdp setup after an AmberTools(ZAFF) -> ParmEd -> GROMACS handover
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0
|
18
|
October 13, 2026
|
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Low GROMACS Performance on RTX 5090 Workstation
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4
|
304
|
August 31, 2026
|
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Tabulated function for 1-4 interactions
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1
|
67
|
August 25, 2026
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MDrun: Simulation speed jumping a factor of 10 with a gpu executable
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6
|
99
|
August 24, 2026
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Loss of performance in v. 2021
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27
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1963
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August 24, 2026
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"Accelerating molecular dynamics simulations using fast Ewald summation with prolates" paper
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6
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251
|
August 13, 2026
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RTX 5070 Not Utilized
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3
|
745
|
August 1, 2026
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Multiple gmx processes on GPU(s) ran too slowly
|
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10
|
216
|
July 13, 2026
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Gromacs warning when calculating RMSD: excessively large distances exist or the system is exploding
|
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1
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45
|
June 24, 2026
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Fatal Error: no domain decomposition for rank 4, min cell size 1.776 nm
|
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1
|
51
|
June 24, 2026
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WT vs mutant protein-protein complex MD: should mutant be generated from WT docked complex or redock
|
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0
|
37
|
June 15, 2026
|
|
What if the protein contains mutations and missing residues?
|
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2
|
132
|
June 4, 2026
|
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Box changing shape after equilibration
|
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8
|
177
|
May 26, 2026
|
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How to solve inconsistent shifts over periodic boundaries in protein-dna run in minimization step?
|
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11
|
3141
|
May 17, 2026
|
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Segmentation fault without further information
|
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3
|
92
|
May 13, 2026
|
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Colvars: Error: keyword "customfunction" is not supported
|
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3
|
214
|
May 12, 2026
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LINCS Error in production run
|
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2
|
171
|
May 1, 2026
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Mdrun with awh for a dimeric protein
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0
|
53
|
April 29, 2026
|
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Energy calculations during mdrun with multiple groups
|
|
2
|
70
|
April 23, 2026
|
|
Extreme performance loss with version 2026.1 on APUs
|
|
10
|
233
|
April 13, 2026
|
|
GROMACS Command for Minimization, Equilibration, Production Runs from CHARMM README
|
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0
|
64
|
April 4, 2026
|
|
Abnormal dVremain/dl values in GROMACS 2025.0 with vdw-type=pme and free-energy
|
|
3
|
47
|
March 31, 2026
|
|
Issues regarding MDrun in HPC
|
|
0
|
34
|
March 26, 2026
|
|
Coulomb (SR) calculation in PME
|
|
9
|
139
|
March 19, 2026
|
|
Steered Molecular dynamics of a ligand moving towards bilayer membrane
|
|
1
|
85
|
March 16, 2026
|
|
Paradoxical Density in OPLS-AA: Diesel mixture density is abnormally LOWER than its lightest compone
|
|
6
|
101
|
March 15, 2026
|
|
Restart MD run from a particular time moment in *.xtc file?
|
|
5
|
124
|
March 6, 2026
|
|
Gromacs-CP2k energy minimization
|
|
0
|
51
|
February 24, 2026
|
|
Steered MD Simulation error
|
|
19
|
350
|
February 19, 2026
|
|
Equilibration not work
|
|
0
|
37
|
February 17, 2026
|