[gmx-users] the temperature effect in the simulation
Mu Yuguang (Dr)
YGMu at ntu.edu.sg
Tue Nov 11 21:17:57 CET 2008
Do you have water ?
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Nicolas Sapay
Sent: 2008年11月12日 4:15
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the temperature effect in the simulation
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.
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