[gmx-users] Timestep in GROMACS simulation

Hi all, How did you choose your timestep and simulation time when running GROMACS? Is there any logic for deciding that? I’ve read that larger time step permits better sampling without significant errors in observed thermodynamic, structural or dynamic properties => What does “sampling” mean? Why

Re: [gmx-users] Timestep in GROMACS simulation

Hi, That totally depends on your forcefield. Most classical all-atom forcefields are recommended to be run with a 2 femtosecond timestep. Some coarse-grained forcefields like Martini can do 20+ fs, but you’ll want to check the literature. As for better sampling, you simply sample longer times for

Re: [gmx-users] Timestep in GROMACS simulation

Hi, I'm still not clear what "sampling" means. Does it mean collecting data from the simulation? Thank you very much for your answer. Best, Anh Vo -Original Message- > > > Message: 4 > > Date: Tue, 28 May 2019 20:43:32 -0400 > > From: Kevin Boyd > > > > Hi, > > > > That totally depe

Re: [gmx-users] Timestep in GROMACS simulation

Hi, > I'm still not clear what "sampling" means. Does it mean collecting data > from the simulation? Pretty much. The point of a molecular dynamics simulation is to calculate structural, thermodynamic, etc... properties of some system from the microscopic dynamics of atoms/molecules/whatever. Col