[gmx-users] unstable system

Shima Arasteh shima_arasteh2001 at yahoo.com
Sun Apr 7 07:41:39 CEST 2013

Hi all,

 I have a system of peptide/POPC/water/ions. The energy minimization and NVT steps has passed successfully. I ran NPT step for around 10 ns with restraints of protein and P atoms at first nano seconds and then removing them gradually. 
I tried to go on MDRUN. I did not remove restraint of protein atoms completely and they are still restrained. When I run the mdrun command, I get error of "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group" .
I know this error means an unstable system. When I visualized the written pdb files, I see some popc hydrogen atoms are broken and located between two leaflets which are separated by a gap. The protein seems ok, however I  don't get many pdb files to see.

As what I see in Diagnosing unstable system web page,
1. it would be beneficial if one see what part of the system is unstable in first steps. As I saw, the unstable "POPC hydrogen atoms" are not fine.
2. The single molecules are supposed to examine in water or vacuum too. I have passed this step successfully.
3. I have not ignored any warning during the last steps.
4. And my mdp files to run md is as follow:

integrator    = md        
dt        = 0.002      
nsteps        = 5000000    

ns_type        = grid        
nstlist        = 5       
rlist        = 1.2       
rlistlong       = 1.4
rcoulomb    = 1.2        
rvdw        = 1.2       
pbc        = xyz        
vdwtype         = switch
rvdw_switch     = 0.1
; Parameters for treating bonded interactions
continuation    = yes       
constraint_algorithm = LINCS    NCS / SHAKE)
constraints    = all-bonds    )
lincs_iter    = 1        
lincs_order    = 4      

; Parameters for treating electrostatic interactions
coulombtype    = PME        ; Long range electrostatic interactions treatment (cut-off, Ewald, PME)
pme_order    = 4        ; Interpolation order for PME (cubic interpolation is represented by 4)
fourierspacing    = 0.16        ; Maximum grid spacing for FFT grid using PME (nm)

; Temperature coupling parameters
tcoupl        = Nose-Hoover            
tc-grps        = Protein_POPC Water_and_ions        ; Define groups to be coupled separately to temperature bath
tau_t        = 0.5    0.5             ; Group-wise coupling time constant (ps)
ref_t        = 310     310        ; Group-wise reference temperature (K)

; Pressure coupling parameters
pcoupl        = Parrinello-Rahman      
pcoupltype    = semiisotropic            
tau_p        = 2.0                
ref_p        = 1.01325 1.01325       
compressibility = 4.5e-5    4.5e-5     

; Miscellaneous control parameters
; Dispersion correction
DispCorr    = EnerPres      
; Initial Velocity Generation
gen_vel        = no          
; Centre of mass (COM) motion removal relative to the specified groups
nstcomm        = 1           y (steps)
comm_mode    = Linear      
comm_grps    =Protein_POPC Water_and_ions    ; COM removal relative to the specified groups

 Would you please let me know if these happen due to an improper equilibration? Do I need to extend the NPT step? Would that fix it?

Thanks in advance. I appreciate your suggestions.


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