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How to determine the number of Hydrogen bonds between the amide H and carbonyl oxygen
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0
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40
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September 28, 2025
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Homocysteine covalently bonded with a protein MD simulation how to perform
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0
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44
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July 21, 2025
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RMSF values are different for same residues, same trajectory
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0
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43
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June 6, 2025
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Simulating tripeptide with D-Amino Acids
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0
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43
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April 23, 2025
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High pressure in x and y axis in a buble in a nano channel
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2
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30
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January 5, 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
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24
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March 15, 2026
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Colvars' distancePairs to get minimum distance between molecules
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1
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32
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December 30, 2025
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Mdrun log file error Large VCM(group MEMB)
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1
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31
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August 11, 2025
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Potentials in topology file
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1
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31
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April 9, 2025
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A Custom Water Force Field Implementation
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0
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46
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October 17, 2025
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Fatal error: Residue 175 named GLU of a molecule in the input file was mapped to an entry in the top
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0
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39
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May 18, 2025
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4th March, bi-weekly GROMACS meeting - evening edition
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1
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40
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March 3, 2026
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Umbrella sampling for a protien ligand system
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1
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32
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January 29, 2026
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What is the exact command to run a (CHARMM-GUI) step6.1_equilibration.cpt Checkpoint File?
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2
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35
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March 31, 2026
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CGenFF ligand: No default bond/angle/dihedral types error in GROMACS
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4
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20
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March 18, 2026
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Struggling to replicate free energy calculations in pmx tutorial using FEP
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0
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45
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January 26, 2026
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GROMACS 2025.4 patch release
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0
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39
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November 21, 2025
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Water quantity in simulation box
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0
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39
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August 22, 2025
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Potentials on gromacs
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0
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40
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May 16, 2025
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Calculating RMSD from an extended run
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0
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44
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May 7, 2025
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Feature Request——Hope that Acceleration can be calculated with GPU
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0
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39
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April 14, 2025
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Non-integer total charge after partial charge replacement for a covalent Cys–maleimide patch
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0
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39
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December 31, 2025
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Ligand jumping from the box
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0
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37
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October 30, 2025
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Free energy landscape diagram
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0
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38
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August 19, 2025
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MMPBSA for custom atom types
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0
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40
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July 20, 2025
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Confusion over RB and Fourier Dihedrals
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0
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39
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May 29, 2025
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Gmx dipoles and index groups vs molecules
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0
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45
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April 24, 2025
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Pull code (umbrella, distance): Fatal error "Pull reference distance … needs to be non-negative"
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1
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35
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February 11, 2026
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23rd July, biweekly GROMACS developer meeting - afternoon edition
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1
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30
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July 23, 2025
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Problem using Position restraints for multiple groups
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2
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24
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March 30, 2026
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18th March, bi-weekly GROMACS meeting - morning edition
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3
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21
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March 18, 2026
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How to generate topology and .itp files for succinic acid and Zn²⁺ in GROMACS using OPLS-AA?
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0
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39
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August 28, 2025
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Constrain receptor ligand
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0
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37
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June 28, 2025
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About energy in gromacs
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0
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39
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June 27, 2025
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ERROR 1 [file dd.itp, line 198]: No default Proper Dih. types
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0
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37
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May 19, 2025
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Regarding missing atomtypes in oplsaa
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0
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38
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April 6, 2025
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Multicomponent system
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1
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29
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April 1, 2026
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Gromacs2026.0, Large number of warnings when building with cray programing environments (CPE25.02)
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1
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34
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February 11, 2026
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Colvars: get topol chain names to match make_ndx
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1
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31
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October 10, 2025
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Gmx sham can not generate xpm file
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0
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35
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August 1, 2025
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Acpype converting dihedral barrier units from kJ/mol to kcal/mol
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0
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40
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May 21, 2025
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Equivalent to the old sas2mat
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0
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43
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April 17, 2025
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How to add hydrogen atoms to the complex with correct coordinates?
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2
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25
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January 23, 2026
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Resuming run with -cpi fails when launched with mpiexec.hydra -np $SLURM_NPROCS
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0
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37
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October 16, 2025
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Md simulate
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0
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36
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August 21, 2025
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Umbrella sampling of ligand pulling towards binding site
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0
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36
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August 3, 2025
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Studying Zn2+ tetrahedal coordination stability
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0
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35
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May 21, 2025
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Charmm36 included non-standard aminoacid
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0
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37
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April 18, 2025
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Changing the group name in gmx make_ndx
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1
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25
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March 3, 2026
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RNA simulation error solution, especially during topology and em.tpr generation
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1
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27
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December 3, 2025
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