From: Marc Q. Ma (qma_at_oak.njit.edu)
Date: Wed Aug 03 2005 - 14:57:26 CDT
It is not wrong to use 1fs for rigid bonds. MD simulations of rigid
waters permit 2fs timesteps. However, the smaller the time steps you
use, the more accurate results you will get from solving the ODEs that
govern the motion of the particles in the system.
I would suggest you use 2fs timesteps for your rigid-bonds simulations
unless you have other reasons for not doing so -- such as you were
concerned about accuracy of short trajectories rather than stability of
long trajectories. Due to the chaotic nature of MD systems, you do not
get "accurate" results of "long" trajectories anyway. Meanwhile, if you
are doing long simulations, you can save half of the time by choosing a
stepsize of 2fs instead of 1.
On Aug 3, 2005, at 2:45 PM, Stern, Julie wrote:
> Is it wrong to have a timestep of 1 fs
> for rigid bonds if it is only applied to
> waters? Is it still supposed to be at 2 fs.
> The program didn't complain, but I believe it
> does complain if its 1 fs and rigidBond all.
> Please advise. thanks.
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