[gmx-users] Protein in vacum

Shima Arasteh shima_arasteh2001 at yahoo.com
Mon Jan 28 10:47:46 CET 2013

Dear users,

I have done simulation with my protein in water earlier successfully using CHARMM36 FF. Now, I am trying to simulate protein in vacum similar to the last simulation of protein-water. When I go to the NPT equilibration, I get a fatal error.
The commands I ran:

1.pdb2gmx -f monomer.pdb -o monomer.gro  -ter
2.editconf -f monomer.gro -o monomer_newbox.gro -c -d 1.0 -bt cubic
3.grompp -f EM.mdp -c monomer_solv_ions.gro -p topol.top -o EM.tpr
4.mdrun -v -deffnm EM
Steepest Descents converged to Fmax < 100 in 1632 steps
Potential Energy  = -2.3169937e+02
Maximum force     =  9.9520912e+01 on atom 360
Norm of force     =  1.9172571e+01

5.grompp -f NVT.mdp -c EM.gro -p topol.top -o NVT.tpr
6.mdrun -deffnm NVT -v

7.grompp -f NPT.mdp -c NVT.gro -t NVT.cpt -p topol.top -o NPT.tpr
8.mdrun -v -deffnm NPT
Fatal error:
The X-size
of the box (3.202905) times the triclinic skew factor (1.000000) is smaller than the number of DD cells (4) times the smallest allowed cell size (0.800718)

The npt.mdp file settings are:
; Parameters describing neighbors searching and details about interaction calculations
ns_type        = grid        ; Neighbor list search method (simple, grid)
nstlist        = 5        ; Neighbor list update frequency (after every given number of steps)
rlist        = 1.2        ; Neighbor list search cut-off distance (nm)
rlistlong       = 1.4
rcoulomb        = 1.2           ; short-range electrostatic cutoff (in
rvdw            = 1.2           ; short-range van der Waals cutoff (in nm)
vdwtype         = switch
rvdw_switch     = 0.8
; Parameters for treating bonded interactions
continuation    = no        ; Whether a fresh start or a continuation from a previous run (yes/no)
constraint_algorithm = LINCS    ; Constraint algorithm (LINCS / SHAKE)
constraints    = all-bonds    ; Which bonds/angles to constrain (all-bonds / hbonds / none / all-angles / h-angles)
lincs_iter    = 1        ; Number of iterations to correct for rotational lengthening in LINCS (related to accuracy)
lincs_order    = 4   
    ; Highest order in the expansion of the constraint coupling matrix (related to accuracy)

; 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            ; Modified Berendsen thermostat using velocity rescaling
tc-grps        = Protein     ; Define groups to be coupled separately to temperature
tau_t        = 0.5            ; Group-wise coupling time constant (ps)
ref_t        = 310             ; Group-wise reference temperature (K)

; Pressure coupling parameters
pcoupl        = Parrinello-Rahman        ; Pressure coupler used under NPT conditions
pcoupltype    = isotropic            ; Isotropic scaling in the x-y direction, independent of the z direction
tau_p        = 5.0                ; Coupling time constant (ps)
ref_p        = 1.0                ; Reference pressure
for coupling, x-y, z directions (bar)
compressibility = 4.5e-5    4.5e-5        ; Isothermal compressibility (bar^-1)
refcoord_scaling = com
; Miscellaneous control parameters
; Dispersion correction
DispCorr    = EnerPres        ; Dispersion corrections for Energy and Pressure for vdW cut-off
; Initial Velocity Generation
gen_vel        = no            ; Velocity is read from the previous run
; Centre of mass (COM) motion removal relative to the specified groups
nstcomm        = 1            ; COM removal frequency (steps)
comm_mode    = Linear        ; Remove COM translation (linear / angular / no)
comm_grps    = Protein
    ; COM removal relative to the specified groups

Would you please help me? How would it be possible to solve my problem?

Thanks in advance.


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