GROMACS version: 2020 GROMACS modification: No Here post your question Dear Users, I have been trying to run a protein bound nanosheet in gromacs. I follow the same protocol as given in the protein-ligand simuation. Initial minimization and equilibration, I perform in my local system and then for production simulation I use a supercomputer. The initial part runs well in my syst…

GROMACS version:2021 GROMACS modification: Yes/No I want to simulate CNT as QM / MM molecular simulation via Gromacs-Gaussian to see the interaction with ions (pi-cation). All ions are defined as molecular mechanics, and only CNT is defined as a quantum part. Is the definition of just CNT as a quantum part enough to see the pi-cation (sodium and magnesium) interaction? …

GROMACS version: 2021.5 GROMACS modification: No As a win10 user I can compile gromacs 2020.6 but I can’t do this on new gromacs requires c++17 with cmake-gui, how can I change ‘-std:c++17’—>‘std=c++17’ in cmake or msvc… (If topic is not related for this forum u can delete it) 1 post - 1 participant Read full topic

Can anyone please help me in how to reduce size of my .xtc files generated after the SMD simulations… And please let me know, is there any effect on the data in .xtc files, when they are compressed. 1 post - 1 participant Read full topic

GROMACS version: 2020 GROMACS modification: No In the documentation for the gmx chi program, we are told that to solve the problem of periodicity in the angles, the autocorrelation functions of the torsions are calculated, i.e. C(t) = <cos(chi(tau)) cos(chi(tau+t))>. The relevant reference is Van der Spoel & Berendsen (1997), Biophys. J. 72, 2032-2041). However, in tha…

GROMACS version: 2020.2-dev-20200430-5e78835-unkown GROMACS modification: GROMACS | NVIDIA NGC I’m performing protein-bilayer simulations of ~360k atoms on a cluster running a docker image of gromacs 2020.2 from nvcr.io Since GPUs are my most limited resource I’m running on a single NVIDIA Quadro RTX 6000 GPU with 16 Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz CPUs. My performance …

GROMACS version: 2020.1 GROMACS modification: No I encountered an error message like this while running the adding ions step, previously I used the pdb2pqr server to change the pH of my protein.pdb . I want to do a molecular dynamics simulation with variations in protein pH, in the hope of getting different rmsd results for each pH variation. Thank you in advance Command line: …

GROMACS version:2016.3 GROMACS modification: No Here post your question Hello, I wanted to model the drug-bound c-Src kinase with the dasatinib bound drug (RCSB: 3G5D) in GROMACS. For dasatinib parameters, I used the parameter values provided in Supplementary Information of “Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Kinase” (Figure attached). I h…