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Keeping the center of mass of a certain group at the center of the box during the simulation process
|
|
1
|
205
|
February 21, 2024
|
|
Does Lipid get Displaced Due to Membrane Protein's Open Conformation? Flexible Cell Approach needed?
|
|
3
|
150
|
February 20, 2024
|
|
Rotational Kinetic Energy after Electric field
|
|
0
|
139
|
February 20, 2024
|
|
Gmx selection of COM residue
|
|
0
|
236
|
February 20, 2024
|
|
Periodic Boundary Conditions Error, Molecule Trajectory Collapses to 2D
|
|
2
|
397
|
February 20, 2024
|
|
MD of ionic supramolecular complex
|
|
1
|
168
|
February 20, 2024
|
|
Free GPU to run Gromacs
|
|
5
|
244
|
February 20, 2024
|
|
Gromacs 2024 MdrunIOTests Failed
|
|
4
|
200
|
February 20, 2024
|
|
GROMACS performance on 8 cores workstation
|
|
8
|
1637
|
February 20, 2024
|
|
Expecting conformational change for protein-DNA complex
|
|
2
|
134
|
February 20, 2024
|
|
Simulation of model Liquid Crystal
|
|
3
|
210
|
February 20, 2024
|
|
Help with simulated annealing of a small peptide
|
|
1
|
519
|
February 20, 2024
|
|
PACKMOL and gmx2pdb
|
|
0
|
346
|
February 20, 2024
|
|
Issue after running 'make' version 2024
|
|
3
|
459
|
February 19, 2024
|
|
Inquiry Regarding Differences in Protein Centering Behavior between Amber and GROMACS
|
|
5
|
252
|
February 19, 2024
|
|
CHARMM parameterization destroys ligand structure
|
|
0
|
213
|
February 19, 2024
|
|
Position restrains in minimization and equilibration
|
|
0
|
209
|
February 19, 2024
|
|
Correcting the pdb file manually
|
|
0
|
148
|
February 19, 2024
|
|
Segmentation fault when running an NPT
|
|
4
|
452
|
February 19, 2024
|
|
Ligand ff based on exsiting ligand ff (which way is faster)
|
|
4
|
161
|
February 19, 2024
|
|
Problem in topology file
|
|
2
|
246
|
February 18, 2024
|
|
Using PMF as an effective potential for coarse grained systems
|
|
0
|
112
|
February 18, 2024
|
|
Error in ion neutralization step
|
|
3
|
131
|
February 18, 2024
|
|
Unstable installation of GROMACS with CUDA toolkit
|
|
1
|
255
|
February 17, 2024
|
|
Dumps in protein_lig of RMSD after MD Simulations
|
|
11
|
359
|
February 17, 2024
|
|
Implausible values in free energy calculations
|
|
4
|
314
|
February 16, 2024
|
|
Overiding bonded parameters from ffbonded.itp by explicitly specifying in residue.rtp
|
|
0
|
205
|
February 16, 2024
|
|
Gmx wham Umbrella Sampling
|
|
2
|
316
|
February 16, 2024
|
|
The issue of constructing the Charmm36 force field for Alpha Synuclein + Monolayer Graphene
|
|
0
|
170
|
February 16, 2024
|
|
Simulating a Protein-Ligand dimer
|
|
6
|
605
|
February 16, 2024
|