GROMACS version: 2021.4 GROMACS modification: Yes/No Here post your question : In building a biphasic system, of cyclohexane-water, while preparing an equilibrated box of cyclohexane, I used the isothermal compressibility of cyclohexane in the .mdp files. But after building the biphase and centering the protein, we need to go for energy minimization, equilibration and final md ru…

GROMACS version:2021.7 GROMACS modification: Yes- plumed patched Hi, I have few doubts in GMX-REST2 and I am posting it below: I have done REST2 simulation with 12 replicas. I would like to know if the output .edr file prints the energy in the scaled format or is it unscaled? Why are we patching PLUMED with GMX? and what is the role of PLUMED In REST2 simulation? I am t…

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Sir, I conducted molecular dynamics (MD) simulations of perylene-derived dimer molecules in acetone and toluene solvents, employing force fields derived from CHARMM-GUI. However, the results deviate from experimental findings. In both solvents, the simulated structures exhibit similar arrangements, contrary to experimental observations where the molecules are close together in ace…

GROMACS version: 2022.3 GROMACS modification: No Dear GROMACS Community Forum, I would like to compute the relative binding free energy change of the protein-ligand complex using Thermodynamic Integration method. Is there any tutorial for using TI method of Protein-ligand complex ? Your suggestions would be highly appreciated. Thanks &Regards Kankana Bhattacharjee Ph.D. …

Hi, I am trying to simulate a material in Gromacs. however, I am using parameters used in lammps. There is a confusing part which is related to the bonds. based on what I read from the article, the bond between Ti and O is at the length of 2.1 A (0.21 nm) and the force constant is 400 Kcal/mol (1673.6 kj/mol). Now the question I have is that what type of bond it is. I searched…