He, Yang wrote:
Hi all users,
When I change the temperature to try to get different disassociation about the
two DNA's strands. But even I change the value of temperature by 0K in the mdp
file ,
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = berendsen
; Groups to couple separately
tc-grps = System
; Time constant (ps) and reference temperature (K)
tau_t = 0.001
The coupling constant sounds a bit small. The dynamics of fast motions
may be affected more than you want, but I'm not a specialist of DNA and
I don't know if it's a problem in that particular case.
ref_t = 300
This indicates that your target temperature is 300K not 0K
; Pressure coupling
Pcoupl = no
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Random seed for Andersen thermostat
andersen_seed = 815131
It will also disassociate .It is strange.
Can anyone of you tell me what is the reason for that?
Thank you in advance.
Yang
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