[gmx-users] huge fluctuation about potential energy: can I reduce it?

[Lixian Zhang]

Dear gromacs users,

I am a beginner for gromacs. Now I try to simulate a stretching behavior of
a simple alpha-helix in aqueous solvent. In this system, the helix consists
of 123 atoms, and SOL molecule is 4281. I adopted afm mode in *.ppa file.
During the simulation, the helix structure is just stretched into a ribbon
structure. So the expected shift of potential energy of system is about
several hundreds kJmol-1, but in the obtained figure (potential energy vs.
time), the fluctuation is huge and even overwhelms the expected shift.

I think this huge fluctuation can be due to the existence of a lot of SOL
molecules. Then the disturbance of system, e.g. thermal, can cause a big
accumulated fluctuation. 

About this problem, can I reduce it using some possible ways? Or is it
inevitable?

Thanks for any help and advice.

Best regards,

Lixian, Zhang

Max Planck Institute for Metals Research
Heisenbergstr. 3
D-70569 Stuttgart
Germany
Tel: +49 (0) 711 689 3578
Email:lixian.zhang at mf.mpg.de 

 

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