[gmx-users] How to estimate the reduced unit temperature?

[David van der Spoel]

DeChang Li wrote:
> Dear gmx-users,
> 
>    I have simulated a Lennard-Jones system that used reduced units. In 
> the system it only contains one atom type B, the non-bonded parameter I 
> wrote below:
> 
> [ nonbond_params ]
>   ; i    j func          c6           c12             sigma           
> epsilon
>     B    B    1 0.400000000   0.400000000   ; --->     1.0000000       
> 0.1000000
>       
>   
> 
> 
> ; Berendsen temperature coupling is on in one groups
> Tcoupl              =  berendsen
> tau_t               =   0.5   
> tc-grps             =  B_atoms
> ref_t               =  10.0    
> 
>    In the simulation I used Berendsen temperature coupling, and set the 
> ref_t = 10. Here I got a reduced temperature T'=0.083, is it right? And 
> if the real interaction strength of atom B is epsilon = 5 KJ/mol, how I 
> can estimate the actual temperature of my simulation system?

T = ref_t/0.083

Chapter 2 in the maual
> 
>    Any suggestions will be help, thank you very much!
> 
> 
>    
> 　　　　　　　　Dechang Li
> 　　　　　　　　Li.DC06 at gmail.com <mailto:Li.DC06 at gmail.com>
> 　　　　　　　　　　2006-11-20
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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