GROMACS version: 2018.9 Hello everyone, I want to isotropically deform the simulation box of my system in order to calculate the bulk modulus. The box is cubic and I need to deform the box at the same rate along all three axis directions. I used the following mdp options: pcoupl = Parrinello-Rahman pcoupltype = anisotropic tau_p …

GROMACS version:2019 GROMACS modification: No Here post your question Hello all, I want to simulate a pre-initiation complex containing 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and eIF5. which has unnatural residues such as 2MG(2-Methyl Guanosine), 1MG,(1-Methyl Guanosine) 1 in it and whenever I try to run the pdb2gmx program to generate t…

GROMACS version: 5.1.1 GROMACS modification: Yes Dear Users, I’m trying to analyze the adsorption desorption affinity of Urea to hydroxyapatite [110] surface. Hydroxyapatite contains Ca, P, O (bonded to P), O (bonded to H), H. All simulations are conducted using CHARMM27 forcefield. Nose-Hoover method is employed for temperature coupling and Parinello-Rahman for pressure couplin…

GROMACS version: 2020.4 GROMACS modification: No Hello, The source code in gmx_energy.cpp calculates the adiabatic bulk modulus (K_s = -V(dp/dV)_S at constant entropy) as the inverse of the isothermal compressibility (beta_T = -(1/V)(dV/dp)_T at constant temperature). However, isn’t the inverse of beta_T actually the isothermal, and not the adiabatic, bulk modulus since applicat…