[gmx-users] General Questions abdout gromacs
mdsimulation at hotmail.com
Thu Nov 17 18:47:08 CET 2005
I have some questions about gromacs:
1- I'm accessing a linux cluster from my PC at my office, when I run a
simulation I have to keeb the PC on up to the end of the run (which takes 10
days sometimes) is there any command in gromacs which enable me to run the
simulation from my PC and keep it working in the cluster no matter wither my
PC is on or off?
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?
3- After running the simulation how can I get the position and the speed of
the moleculs (atoms) at each time output?
4- can I incert a hydrophopic serface into my simulation box? I mean cam I
make one of the simulation box faces a hydrophopic surface, I'm willing to
use Gold as my substrate.
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