To add to what Dave Case said, you need to be careful with shake
setting. In principle, using shake for X-H bonds will make NVE not
really conserve energy.
To check this, set ntc and ntf not to be used, and try very small dt,
maybe 0.5 fs or potentially lower.
Adrian
On 5/9/20 12:38 AM, Liao wrote:
> [External Email]
>
> Dear Amber users,
>
> 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.
> Has anyone else ran into such a situation?
> Thank you.
>
>
>
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--
Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Sat May 09 2020 - 09:00:02 PDT
