[gmx-users] Justin protein-ligand complex...

[Justin A. Lemkul]

rama david wrote:
> Hi Gromacs user ,
>  
>  In justin tutorial protein-ligand complex..
> 
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/08_MD.html
> 
> the production md.mdp has following parameter for Pressure  and 
> Temperature coupling 
> 
> ; Temperature coupling is on
> tcoupl      = V-rescale                     ; modified Berendsen thermostat
> tc-grps     = Protein_JZ4 Water_and_ions    ; two coupling groups - more accurate
> tau_t       = 0.1   0.1                     ; time constant, in ps
> ref_t       = 300   300                     ; reference temperature, one for each group, in K
> ; Pressure coupling is off
> pcoupl      = Parrinello-Rahman             ; pressure coupling is on for NPT
> pcoupltype  = isotropic                     ; uniform scaling of box vectors
> tau_p       = 2.0                           ; time constant, in ps
> ref_p       = 1.0                           ; reference pressure, in bar
> compressibility = 4.5e-5                    ; isothermal compressibility of water, bar^-1
> ; Periodic boundary conditions
> pbc         = xyz       ; 3-D PBC
> 
> 
> 
> My query is ..Why Pressure Coupling is off  in  production MD run ???
> 

Pressure coupling is on, hence:

pcoupl      = Parrinello-Rahman

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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