[gmx-users] General Questions abdout gromacs

[Marcus Kubitzki]

> 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?
g_traj

Cheers,
Marcus

-- 
Marcus Kubitzki
Max Planck Institute for Biophysical Chemistry
Computational Biomolecular Dynamics Group
Am Fassberg 11
D-37077 Göttingen
Germany
phone: ++49-551-2012312
fax: ++49-551-2012302
Email: mkubitz[at]gwdg.de
www: http://www.mpibpc.mpg.de/groups/de_groot/