Hi all, 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 are:
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, Xiu Peng.
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