[gmx-users] calculation speed of GROMACS and cut off parameters

[mircial at sjtu.edu.cn]

Hi everyone,

I am using GROMACS to simulate bilayers, and I am testing two sets of parameters at present. However, I found significant differences of simulation speed of these two parameters sets. 
The mainly differences between these parameters are the cut off parameters or of the VDW and coulomb interactions, in the first parameter set, a cut off of 1.0 nm was used for both of the VDW and the coulomb interactions. In the second parameter set, a cut off 1.4 was used for the coulomb interactions, whereas a switch from 1.4 nm to 1.5 nm was used for the VDW parameters.  Under the first parameter set, my system could run about 20 ns per day, whereas for the second parameter set, my system only run 7-8 ns per day.  So I am wondering if this is only raised because of the cut off parameters? And is this a normal pheonomen?

I am listing the mdp file at the end of this email. Please note the only relevarent differences between these two parameter sets are the cut off differences. 

With my best regards, 
rxgu
--------------------------------------------
the first parameter set:

title          = NPT Equilibration


integrator     = md
nsteps         = 25000000
dt             = 0.002        
nstxout        = 0          
nstvout        = 0          
nstenergy      = 1000          
nstlog         = 2000          
nstxtcout      = 2000
xtc-precision  = 10000

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

;cutoff-scheme  = Verlet  
ns_type        = grid          
nstlist        = 10          
rlist           = 1.0
          
coulombtype    = PME
rcoulomb       = 1.0                                                                                                                              
                                                                                                                                                  
vdwtype           = cut-off                                                                                                                       
rvdw           = 1.0                                                                                                                              
DispCorr       = EnerPres                                                                                                                         
pme_order      = 4                                                                                                                                
fourierspacing = 0.12                                                                                                                             
optimize_fft   = yes                                                                                                                              
                                                                                                                                                  
pbc            = xyz                                                                                                                              
                                                                                                                                                  
tcoupl         = V-rescale                                                                                                                        
tc-grps        = POPC SOL                                                                                                                         
tau_t           = 0.5   0.5                                                                                                                       
ref_t           = 323  323

pcoupl         = Berendsen      
pcoupltype     = semiisotropic          
tau_p           = 10.0 10.0              
ref_p           = 1.0  1.0          
compressibility = 4.5e-5 4.5e-5          

gen_vel         = yes
gen_temp        = 323
gen_seed        = 82907543

comm-mode       = Linear
comm-grps     = system
----------------------------------------------------------------
the second parameter set:

title          = NPT Equilibration


integrator     = md
nsteps         = 25000000
dt             = 0.002        
nstxout        = 0          
nstvout        = 0          
nstenergy      = 1000          
nstlog         = 2000          
nstxtcout      = 2000
xtc-precision  = 10000

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

;cutoff-scheme  = Verlet  
ns_type        = grid          
nstlist        = 10          
rlist           = 1.4
rlistlong      = 1.7
          
coulombtype    = PME
rcoulomb       = 1.4 
         
vdwtype           = Switch
rvdw           = 1.5
rvdw-switch    = 1.4
DispCorr       = EnerPres
pme_order      = 4          
fourierspacing = 0.12          
optimize_fft   = yes

pbc            = xyz

tcoupl         = V-rescale          
tc-grps        = POPC SOL  
tau_t           = 0.5   0.5            
ref_t           = 323  323

pcoupl         = Berendsen      
pcoupltype     = semiisotropic          
tau_p           = 10.0 10.0              
ref_p           = 1.0  1.0          
compressibility = 4.5e-5 4.5e-5          

gen_vel         = yes
gen_temp        = 323
gen_seed        = 82907543

comm-mode       = Linear
comm-grps       = System 
--------------------------------------------------------------------------------------