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Centering a molecule that crosses periodic boundaries — single-atom trick
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1
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43
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May 18, 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
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3039
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May 17, 2026
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Divalent ion parameterization in GROMACS
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1
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43
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May 13, 2026
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Segmentation fault without further information
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3
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44
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May 13, 2026
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Colvars: Error: keyword "customfunction" is not supported
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3
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184
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May 12, 2026
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Details of viscosity estimation (gmx energy -vis)
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6
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1266
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May 11, 2026
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Mindist usage on multichain systems
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0
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18
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May 11, 2026
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Gmx 2025.4 in Ubuntu 26.04
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3
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73
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May 8, 2026
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Sidechain S square for md data using rotacf
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0
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17
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May 8, 2026
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Order Parmeter S^2 using rotacf
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3
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713
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May 8, 2026
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Duplicates of rows of angles and dihedrals for groups containing Cl
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1
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23
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May 8, 2026
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Error due to line in input file longer than 4095 characters
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9
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1074
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May 7, 2026
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Make not working during gromacs installation
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3
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320
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May 7, 2026
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Install workflow with AMD GPU support (Framework 16, Ubuntu 24.04, GPU: AMD Radeon RX 7700S)
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11
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2701
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May 6, 2026
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Post MD analysis of peptide-membrane interaction
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0
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28
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May 6, 2026
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AWH simulation with cylinder pull geometry
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14
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139
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May 6, 2026
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RMSD shoots up
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18
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1789
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May 5, 2026
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Backmapping CG to AA
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0
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34
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May 3, 2026
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Is PBC correction needed before Peak force, total work, RMSD analysis and trajectory visualization?
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1
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30
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May 2, 2026
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LINCS Error in production run
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2
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128
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May 1, 2026
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"Segmentation fault", "std::bad_alloc" and "malloc(): invalid size" when running gmx hbond
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11
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1308
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April 30, 2026
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Custom Amino Acid Partial Charge Assignment
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0
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20
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April 30, 2026
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Mdrun with awh for a dimeric protein
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0
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35
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April 29, 2026
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How to extract middle cluster structure form gmx_cluster output file cluster.pdb
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0
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34
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April 29, 2026
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PBC/trajectory reconstruction problem for discontinuous multi-chain RNA fragment
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0
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19
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April 28, 2026
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Fatal error: Internal error in LAPACK diagonalization
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6
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58
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April 28, 2026
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Installing gromac in anaconda/spyder environment
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0
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22
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April 28, 2026
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One system not plateauing in NPT before SMD comparison across multiple complexes
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0
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23
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April 28, 2026
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Question Amber19SB and generation of modified residues
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0
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34
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April 26, 2026
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GROMACS SMD for TCR–pMHC: should TCR be pull group 1 or 2
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0
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33
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April 25, 2026
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