[AMBER] why total energy of the system is on the rise in NVE ensemble

From: zhangmk <zhangmk69.gmail.com>
Date: Mon, 13 Oct 2014 10:43:03 +0800

Dear professors:

Recently, I simulated polypeptides in aqueous solution in a 6.8 nm
square system. First, following the tutorial presentations, I do min,
heat, density, equil process.Then the system were calculated in NVT
ensemble for 5 ns to reach balance, the script like this:

Vol Ala30HX2Sol





cut=10.0, ntb=1,

ntpr=20000, ntwx=20000,ntwr=-100000,

ntt=3, gamma_ln=3.0, temp0=310.0,


Finally, a 5ns NVE simulation was conducted, the script follows:

Ene Ala30HX2Sol


imin=0, irest=1, ntx=5,

nstlim=5000000, dt=0.001,

ntb=1, ntt=0,


ntc=2, ntf=2,

ntpr=20000, ntwx=20000,ntwr=-100000,


But in the NVE simulation, I find that the total energy of the system is
on the rise In the attached file, how this thing happened? should be the
ETOT unchanged in NVE?

Chongqing Institute of Green and Intelligent Technology of Chinese 
Academy Sciences.

AMBER mailing list

(image/jpeg attachment: ETOT.jpg)

Received on Sun Oct 12 2014 - 20:00:02 PDT
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