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How to use the forum
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1
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4116
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October 28, 2020
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About the User discussions category
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0
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2104
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April 24, 2020
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RMSD shoots up
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18
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1756
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May 5, 2026
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Backmapping CG to AA
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0
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12
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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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16
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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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106
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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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1268
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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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11
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April 30, 2026
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AWH simulation with cylinder pull geometry
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13
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76
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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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20
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April 29, 2026
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Gmx anaeig problematic error "Dimensions in the eigenvector files don't match"
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0
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15
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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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15
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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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14
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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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42
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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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13
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April 28, 2026
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Calculating the free energy of binding using AWH approach
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6
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63
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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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16
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April 28, 2026
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Details of viscosity estimation (gmx energy -vis)
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5
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1209
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April 27, 2026
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Question Amber19SB and generation of modified residues
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0
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19
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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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24
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April 25, 2026
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Energy calculations during mdrun with multiple groups
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2
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28
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April 23, 2026
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Covalent bound PLP to SPT (membrane bound)
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0
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16
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April 22, 2026
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Unexpected lateral forces in idealised slab system of LJ particles
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1
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25
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April 22, 2026
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Using AWH for bilayer permeability
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18
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1283
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April 22, 2026
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How to use CHARMM-GUI LBS Finder & Refiner output for GROMACS sim to hypothesize binding site
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0
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19
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April 21, 2026
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Peptide-protein MD sumulation
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0
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20
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April 21, 2026
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Scaling factor for surface tension in Reduced Units
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2
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30
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April 19, 2026
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'Two replicas have identical temperatures' error during REST2 simulation in GROMACS 2025"
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1
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20
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April 15, 2026
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Changes of default `nstpcouple` and `nsttcouple` from version 2022 to 2023
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35
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2381
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April 14, 2026
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Extreme performance loss with version 2026.1 on APUs
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10
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112
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April 13, 2026
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