[gmx-users] General Questions abdout gromacs
mkubitz at gwdg.de
Fri Nov 18 10:50:13 CET 2005
> 2- I'm running a simulation for 64 glycine molecules with 449 water
> molecules. I need to run this for the first one second but the time step
> in the .mdp file is 1fs and the program doesn't work if I increase the
> time step. is there any other way I can speed up the simulation?
Simulating your system for one second(!) requires a little bit of
patience. Depending on hardware, ffield & water model a system of ~2000
atoms (my estimate) evolves a few ns/day.
You can increase the time step to 2fs by constraining all bonds using
LINCS or SHAKE.
> 3- After running the simulation how can I get the position and the speed
> of the moleculs (atoms) at each time output?
Max Planck Institute for Biophysical Chemistry
Computational Biomolecular Dynamics Group
Am Fassberg 11
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