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How to simulate d-amino acids by amber force field
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0
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15
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March 1, 2025
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Optimizing Production Run with GPUs and CHARMM36
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3
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55
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February 27, 2025
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Pdb file for more than 70 chains
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2
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23
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February 18, 2025
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Issue with direction-periodic and periodicity during umbrella sampling
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4
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39
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February 17, 2025
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Free energy difference is zero for non-zero coulomb-lambdas during solvation free energy calculation
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3
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31
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February 13, 2025
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How to run a molecule which has O+ in it?
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0
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13
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February 12, 2025
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Segmentation fault in MARTINI 2.2 with pulling
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16
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54
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February 12, 2025
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Position restraints for Umbrella sampling simulation of membrane protein-ligand
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6
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241
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February 11, 2025
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Pull simulations giving LINCS error
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1
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20
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February 11, 2025
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Optimizing CPU/GPU efficiency and performance in GROMACS simulations
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4
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186
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February 11, 2025
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Gromacs in docker image does not work in server
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5
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66
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February 5, 2025
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Unfolding a 574 aa protein
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0
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34
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February 3, 2025
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What is the difference between tensile MD simulation and non-equilibrium MD simulation?
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6
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91
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February 2, 2025
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Unable to generate topology for my ligand
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0
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65
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February 1, 2025
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Dehydrated bilayer simulation
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2
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32
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January 30, 2025
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DNA TOP file
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2
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31
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January 27, 2025
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No default U-B Types
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0
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49
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January 16, 2025
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How to Place a Peptide Near DNA in a Box
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0
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14
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January 27, 2025
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No default bond, dihedrals, angles
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0
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11
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January 27, 2025
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Parametrization of PYROGLUTAMIC ACID
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4
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67
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January 25, 2025
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Advice for setting up attraction potential measurement between 2 collagen triple helices
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0
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6
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January 24, 2025
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Protonation States in the OPLS-AA Forcefield
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0
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14
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January 24, 2025
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How to perform md simulation on a protein structure which have a ca+ ions
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0
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28
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January 23, 2025
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Topology of an ACE-linked cyclic peptide with a free C-ter
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0
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32
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January 23, 2025
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NPT Step Issue with Protein 1QS4 (4 Waters and Mg²⁺ in Active Site)
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4
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28
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January 22, 2025
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Position restraints missing when .itp is printed to .top
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2
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55
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January 21, 2025
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Charges and itp file
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0
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16
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January 21, 2025
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Help, adding PEG to my gro and top file-is not placed where it should be
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4
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43
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January 17, 2025
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Nanoparticle getting disintegrated in MD production after simulated annealing
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0
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22
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January 17, 2025
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How can I add molecules to an equilibrated system without messing PBCs?
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1
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18
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January 16, 2025
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