fufengliu wrote:
Hello, everyone,
I have some questions about ensemble. Would you please tell me about NPT
or NVT ensemble? What difference about them? And how to define in the
molecular dynamics mdp file? What ensemble does the below parameters
extracted from my mdp file?
NPT = constant Number of molecules, Pressure, Temperature
NVT = constant Number of molecules, Volume, Temperature
If you are blindly writing .mdp parameters without knowing what you are doing,
you had better re-think your approach. Your comments in the file will tell you
what you are doing. Sounds like some textbook reading (regarding ensembles)
would be useful, as well as a thorough read of the Gromacs manual to learn what
the options are doing.
-Justin
; Berendsen temperature coupling is on
Tcoupl = berendsen
tau_t = 0.1 0.1
tc-grps = protein non-protein
ref_t = 300 300
; Pressure coupling is on
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
Thank you for your kind consideration of these questions.
Sincerely,
Fufeng Liu
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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