[gmx-users] Time step and constraints
goushenzhiyuan at gmail.com
Wed Feb 27 18:06:25 CET 2008
Recently, I run a peptide with about 110 atoms solvated in a cubic box
with about 1300 rigid TIP3P water molecules. A time step of 2 fs is used.
The constraints are turned off (constraints = none in mdp file). As I know,
a time step of 1 fs is usually used with no constraints. So my questions
1. When I run a peptide simulation, does it make sense if I use a time
step of 2 fs when the constraints are turned off?
2. When the constraints are turned off, the rigid-bond of water
molecules are still maintained by the LINCS algorithm?
Thanks in advance,
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