[gmx-users] RE: average pressure of a system

[Dwey Kauffman]

Hi Dallas and Justin,

  Thanks for the reply. Yes, I did plot pressure changes over time by
g_energy and I have been aware of the note  at
http://www.gromacs.org/Documentation/Terminology/Pressure
  
I am concerned about the average pressure is because our experiment shows
that our target membrane protein is a hexamer and our observation is that
variation of system pressure seems causing hexamer or dimer dissociation.
Also, it is quite sensitive to pressure fluctuation. Such a fluctuation of
pressure certainly brings my attention in this specific case, because life
does not exist at large variations of system pressure.
If not because of multimer dissociation likely caused by pressure
fluctuation, I agree with both of you.

I also run longer simulations like 20 ns and 30 ns

### 20 ns

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Pressure                   0.886396       0.84    162.655    1.38476  (bar)

## 30 ns

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Pressure                    1.69086       0.58    162.879    3.35668  (bar)


Running longer simulations seems to me that the improvement of system
pressure is not helpful too much.
If I need to modify mdp file, what it would be ?



Many thanks,

Dwey


My mdp file for NPT  is used in the simulation like 

define          = -DPOSRES      

integrator      = md            
nsteps          = 500000        
dt                  = 0.002             

nstxout         = 100           
nstvout         = 100           
nstenergy       = 100           
nstlog          = 100           

continuation    = yes               
constraint_algorithm = lincs    
constraints     = all-bonds             
lincs_iter      = 1                         
lincs_order     = 4                         

ns_type         = grid          
nstlist         = 5                 
rlist           = 1.2           
rcoulomb        = 1.2           
rvdw            = 1.2           

coulombtype     = PME           
pme_order       = 4                 
fourierspacing  = 0.16          

tcoupl          = Nose-Hoover               
tc-grps         = Protein DPPC  SOL_CL  
tau_t           = 0.5   0.5     0.5             
ref_t           = 323   323     323             

pcoupl          = Parrinello-Rahman         
pcoupltype      = semiisotropic             
tau_p           = 5.0                           
ref_p           = 1.0   1.0                     
compressibility = 4.5e-5        4.5e-5  

pbc                 = xyz               

DispCorr        = EnerPres      

gen_vel         = no            


nstcomm         = 1
comm-mode       = Linear
comm-grps       = Protein_DPPC SOL_CL

refcoord_scaling = com
cutoff-scheme = Verlet




 



  
  



  



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