Hello, I used the GMX msd -type Z option to calculate the results as shown in figure. I would like to ask how the figure"D [ resname > 1.75] = 0.3775(+/-0.4572)(1e-5 cm ^ 2/s)" is calculated. My X axis is 0-5000 and my y axis is about 0-4.7. The slope is about 4.7 over 5000, which is not close to 0.3775. Thank you. 1 post - 1 participant Read fu…

GROMACS version: 2023.3 with CUDA 12.3 GROMACS modification: No Context: I use GROMACS 2023.3 with CUDA 12.3 on my computer with a single RTX 4090. I simulate bilayer assembly processes for a few hundred nanoseconds; the tasks are relatively computationally demanding. Problem: When I run the simulation (with the “gmx mdrun” command; see example below), the initial estimated t…

Hello, I aim to simulate a single interface consisting of 8340 moles of water and 1400 moles of CCl4 within a cubic box with dimensions of 7.8 x 7.8 x 7.8 nm and a solvent height of 40 nm. I have created a Packmol input file as provided below: tolerance 2.0 filetype pdb output m486-i5cm-box.pdb structure M486.pdb number 1400 inside box 0. 0. -39. 78. 78. -1. end structure s…

I’m trying to set up a constant-force pulling simulation but was a little confused on the difference between setting the mdp parameter pull_coord1_geometry to distance or direction. My understanding is that for distance, the pulling occurs along whichever axis is selected in pull_coord1_dim and for direction, it is pull_coord1_vec that is specified, but in the case of a constant-fo…

GROMACS version: gromacs2021 GROMACS modification: No Hello, I am working on something a little bit theoretical where I would like to know the exact velocity of my particles in order to compare different systems with similar configurations except a minor change. When calculating the difference of velocity for each particle between my 2 systems I observe little fluctuations. I wo…

GROMACS version: GROMACS modification: Yes/No Here post your question Dear All , In order to determine the interaction between a magnesium atom from chlorophyll and a gluamate atom, I performed my QM calculations for geometry scan.I completed my QM calculations for the geometry scan, but here are some specifics: to go further in QMMM approch using Gromacs, there are also one …

Dear Sir, I hope this email finds you well. I am currently facing an issue with my simulation setup and visualization process. To provide context, I have been working on creating a cubic box with acetone solvent for simulation purposes. Initially, I obtained the GROMACS topology using the ligand reader and force field converter in CHARMM-GUI. Subsequently, I constructed a cubic bo…

GROMACS version: GROMACS modification: Yes/No Here post your question: I am trying to calculate free energy profiles of AquaporinZ and its mutants through umbrella sampling. But the pmf curve I got is far more different than the curves I found in previous literature. On left is the reference image and on right (with peaks and energy curve) is the one I got after umbrella sampling…