[gmx-users] unstable system
shima_arasteh2001 at yahoo.com
Sun Apr 7 07:41:39 CEST 2013
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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