On Fri, May 08, 2020, Liao wrote:
>
>I realized my simulation temperature, and total energy, keeps on dropping
>with NVE ensemble. (ntt=0, ntb=1 periodic boundaries on). Isn’t it
>suppose to be constant total energy? What’s more mysterious, is that this
>only happens when I started using an Hydrogens-mass-repartitioned (HMR)
>parmtop file.
Using HMR and a 4 fs time step will generally not conserve energy in
NVE. Energy conservation is roughly proportional to dt**2, at least
anectodally. So, try some experiments with different values of dt to
see what behavior you find in your system.
(It should not be the HMR prmtop that is the problem, but rather the
time step that you are choosing.)
....dac
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Received on Sat May 09 2020 - 06:30:02 PDT
