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
ref_t = 300
I don't know if this is relevant or not, but a coupling constant of 0.001 is
exceptionally short. What is the timestep in your simulation? Typically one
sees tau_t = 0.1 with a timestep of 0.001-0.002 ps.
; 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.
So the dissociation occurs at 0K and 300K? Sounds like something is
fundamentally flawed with your system setup. How large is your box? What force
field are you using?
-Justin
Can anyone of you tell me what is the reason for that?
Thank you in advance.
Yang
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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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