GROMACS version: 5.1.4 GROMACS modification: No Dear community members, I have completed a protein-ligand simulation for 150 ns using Charmm36 force field in accordance with the tutorials written by Dr. Lemkul. Now that my simulation is over, I am interested in checking whether my protein has seen its periodic image during the course of the simulation. I have used a cubic box, (…

@jalemkul GROMACS version:2022.2 GROMACS modification: No Hi Im doing Protein-NonProtein MD simulation for the first time and following the tutorial(Protein-Ligand Complex) with the same example files. I am following the tutorial as it is but facing a few problems. The "jz4.gro" gives a distorted structure (shown below). while the program gmx editconf -f jz4_ini.pdb -o jz4.gr…

GROMACS version: GROMACS modification: Yes/No Here post your question Hello, I want to calculate viscosity of water from periodic perturbation method. I am using the simulation protocol same as that given in this paper Cookie Absent. However, the amplitude of cos velocity profile and hence viscosity I am getting from gmx energy are negative. Also when I calculate x-direction vel…

Hello everyone, my name is Antonio Franco, I am at Campbellsville University doing research about the protein KCNE 3. My labor is to create a SMALP copolymer around this protein making a lipodisq of nanoparticles. I have been doing research on this topic but I haven’t found any type of paper or explanation about creating and running the simulation of the lipodisq, I would like to k…

I am currently investigating reproduction of solubility using a variety of methods. I have carried out free energy simulations using the bulk crystal structure and a range of solution concentrations. A range of solubility has been determined from direct coexistence simulations of a slab exposed to sub- or supersaturated solution. The free energy and DC methods don’t agree with each…

GROMACS version: GROMACS modification: No During any trajectory simulation, does GROMACS calculate the position and momenta of each water molecules using force applied to that particular water solvent molecule? Or all water solvent molecules are randomly generated at each steps (while position and momenta of each atoms in solute molecules are influenced by the force exerted by th…