[gmx-users] Simulation in vacuum
b.mijiddorj at gmail.com
Fri Jan 20 11:01:22 CET 2017
Dear gmx users,
I would like to get experience of simulation in vacuum. Please suggest me
tutorials, and advice me.
I read about following comments which written on Shourjiya Sanyal tutorial.
Can you discuss about it?
In vacuum simulation, integration should be reduced compared to solvent
phase simulation. Periodic boundary conditions, non-bonded interaction
cutoffs, temperature coupling and pressure coupling were all turned off.
Center of mass translation and rotation around the center of mass are to be
removed to avoid the fast spin of the protein. One should also constrain
the hydrogen bond using algorithms like SHAKE/LINCS.
More information about the gromacs.org_gmx-users