[gmx-users] Dubious results with NPT

[sujith]

Dear GROMACS users,

     I am new to GROMACS, and recently started using the version 4.6.5.
   
I have seen a lot of NPT related issues raised earlier in this forum, but in
my case the error looks much more severe.
 
I am following Justin Lemkul's tutorial
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/01_genconf.html)
on Biphasic system, containing cyclohexane and water.Everything went well
till the  NPT simulation to bring system to reference pressure of 1 bar.  

Here are the details of the system , .mdp file , what I did and  where I
find the problem.

   SYSTEM :  512 cyclohexane + 2720 water molecules.
 
   CURRENT STATUS:

             (1)    Energy minimization  : energy converged.

             (2)    NVT (tcoupl=berendsen , tau_t=0.1ps / ref_t=298K)
completed and target pressure of 298 K attained.

             (3)    NPT (tcoupl=nose-hoover, tau_t=0.5ps / pcoupl=berendsen,
tau_p=1ps / ref_p = 1bar , total time=15 ns) completed with the  following 
result:

             Energy                      Average   Err.Est.       RMSD 
Tot-Drift
              
-------------------------------------------------------------------------------
             Pressure                    1.08924       0.67     114.66  
-1.74033  (bar)

        Since berendsen barostat doesn't generate the true ensemble, an
equilibration with  pcoupl=parrinello-rahman is  performed in the next step.

             (4)  NPT (pcoupl=parrinello-rahman, tau_p=5ps, total time=5ns)
----> PROBLEM FACED:  The average pressure too high as shown below which I
feel is not going to improve.

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Pressure                    23.6651       0.53    144.464   -1.00634  (bar)



  I am aware of the fact that pressure is subject to large fluctuations in
small sized systems and that this may affect the average value of the
pressure. But , here the average pressure looks too large to be ignored. The
pressure-vs-time graph doesn't show any upward trend, and the pressure looks 
like fluctuating about a central value.
   
 
                      Here is the .mdp file. Only changes made from the
previous .mdp  for berendsen pressure coupling , are with  pcoupl and tau_p.

; 7.3.3 Run Control
integrator               = md                  
tinit                       = 0                    
dt                         = 0.002                
nsteps                  = 2500000              
comm_mode         = Linear              
nstcomm              = 1                    
comm_grps           = CHX SOL              

; 7.3.8 Output Control
nstxout                 = 2500        
nstvout                 = 2500          
nstfout                  = 2500        
nstlog                   = 2500        
nstenergy              = 100        
nstxtcout               = 1000        
xtc_precision          = 1000        
xtc_grps                = System      
energygrps             = System      

; 7.3.9 Neighbor Searching
nstlist                   = 1            
ns_type                = grid        
pbc                      = xyz        
rlist                      = 0.8        

; 7.3.10 Electrostatics
coulombtype             = PME      
rcoulomb                  = 0.8        
; 7.3.11 VdW
vdwtype                 = cut-off    
rvdw                      = 0.8          
DispCorr                = EnerPres      
; 7.3.13 Ewald
fourierspacing          = 0.12        
pme_order               = 4          
ewald_rtol               = 1e-5        

; 7.3.14 Temperature Coupling
tcoupl                   = nose-hoover                  
tc_grps                 = CHX        SOL            
tau_t                    = 0.5        0.5                
ref_t                    = 298        298              

; 7.3.15 Pressure Coupling
pcoupl                    = parrinello-rahman    
pcoupltype              = isotropic            
tau_p                      = 5.0                  
compressibility        = 4.5e-5                
ref_p                       = 1.0                  

; 7.3.17 Velocity Generation
gen_vel                  = no          

; 7.3.18 Bonds
constraints                 = all-bonds  
constraint_algorithm    = LINCS        
continuation               = yes          
lincs_order                 = 4            
lincs_iter                    = 1            
lincs_warnangle          = 30          
"npt.mdp" 63L, 4080C                                                                                                  
               
    I guess there is something seriously wrong in the choice of
methods/parameters in the .mdp file, which I cant figure out. Kindly go
through and let me know your comments.
I would be happy to give any further details. Any help would be appreciated.                    
                                   
   Regards,
   Sujith 

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