[gmx-users] Warning/Error message in NVT & NPT

[Wui Zhuan Lim]

Hi all,

I'm a beginner in using Gromacs and MD simulation works.
I am currently doing a simulation of enzyme unfolding.
When I began NVT equilibration, a warning note appeared, as shown below:
With twin range cut-offs and SHAKE the virial and pressure are incorrect.
At first, I tried to ignore the warning with -maxwarn (although it's better not to use it, just have a try)
The warning did disappear.
As
 I move forward to NPT, the same message appeared again. But it's no 
longer "warning", but "error" instead, which cannot be avoided with 
-maxwarn, so I could not proceed NPT at the moment.
So I was 
wondering if it's a serious issue to fix it. I understand what twin 
range cut-offs and SHAKE are, but how will I know the appropriate virial
 and pressure?

Regards, 
Adam

**Below are my mdp files for NVT and NPT:

NVT

title       = Protein-ligand complex NVT equilibration 
define      = -DPOSRES  
; Run parameters
integrator  = sd        
nsteps      = 10000     
dt          = 0.002    
; Output control
nstxout     = 100       
nstvout     = 100       
nstenergy   = 100      
nstlog      = 100       
energygrps  = Protein Non-Protein
; Bond parameters
continuation    = no            
constraint_algorithm = shake    
constraints     = hbonds        
; Neighborsearching
ns_type     = grid      
nstlist     = 5        
rlist       = 0.9       
rcoulomb    = 0.9       
rvdw        = 1.4       
; Electrostatics
coulombtype     = PME       
pme_order       = 3         
fourierspacing  = 0.16      
; Temperature coupling                    
tc_grps     = Protein Water_and_ions       
tau_t       = 0.1   0.1                     
ref_t       = 300   300                     
; Pressure coupling
pcoupl      = no        
; Periodic boundary conditions
pbc         = xyz       
; Dispersion correction
DispCorr    = EnerPres  
; Velocity generation
gen_vel     = yes       
gen_temp    = 300      
gen_seed    = -1        



NPT

title       = Protein-ligand complex NVT equilibration 
define      = -DPOSRES  
; Run parameters
integrator  = sd        
ld_seed     = -1
nsteps      = 2500000   
dt          = 0.002     ; 2 fs
; Output control
nstxout     = 100       
nstvout     = 100       
nstenergy   = 100       
nstlog      = 100       
energygrps  = Protein Non-Protein
; Bond parameters
continuation    = no            
constraint_algorithm = shake    
constraints     = hbonds        
shake_tol       = 0.0000001
; Neighborsearching
ns_type     = grid      
nstlist     = 5         
rlist       = 0.9       
rcoulomb    = 0.9       
rvdw        = 1.4       
; Electrostatics
coulombtype     = PME      
pme_order       = 3         
fourierspacing  = 0.16      
; Temperature coupling                  
tc_grps     = Protein Water_and_ions    
tau_t       = 0.1   0.1                 
ref_t       = 300   300                 
; Pressure coupling
pcoupl      = Berendsen                     
pcoupltype  = isotropic                     
tau_p       = 2.0                          
ref_p       = 1.0                           
compressibility = 4.5e-5                    
refcoord_scaling    = com
; Periodic boundary conditions
pbc         = xyz      
; Dispersion correction
DispCorr    = EnerPres  
; Velocity generation
gen_vel     = yes       
gen_temp    = 300       
gen_seed    = -1