[gmx-users] The simulation of big protein in implicit solvent

[Yi Isaac Yang]

Dear all,

Recently, I want to simulate a big protein (about 90 residues) in GBSA 
implicit solvent using gromacs 5.1.2. However, when I want to perform 
the minimization, the program shows that:

_Fatal error:__
__Domain decomposition does not support simple neighbor searching, use 
grid searching or run with one MPI rank__
__For more information and tips for troubleshooting, please check the 
GROMACS__
__website at http://www.gromacs.org/Documentation/Errors_

And the strange thing is, I can use the mdp file to minimization a small 
protein (6 residues, using the same force field), every thing is OK.

If I delete "ns-type=simple" in mdp file, the minimization of small 
protein is still OK. And the minimization of big protein is still not work:
_
__Fatal error:__
__Domain decomposition does not work with nstlist=0__
__For more information and tips for troubleshooting, please check the 
GROMACS__
__website at http://www.gromacs.org/Documentation/Errors_

As no-cutoff is needed in this simulation, I can't delete "_nstlist=0_".

So you know how to solve this problem?

Thanks in advance and best regards,
Isaac



PS: The mdp file:

; minim.mdp - used as input into grompp to generate em.tpr
integrator      = steep         ; Algorithm (steep = steepest descent 
minimization)
emtol           = 1000.0        ; Stop minimization when the maximum 
force < 1000.0 kJ/mol/nm
emstep          = 0.01          ; Energy step size
nsteps          = 50000         ; Maximum number of (minimization) steps 
to perform

; Parameters describing how to find the neighbors of each atom and how 
to calculate the interactions
cutoff_scheme = group   ; Method of managing neighbor lists
pbc           = no      ; Periodic boundary conditions disabled
coulombtype   = cut-off ; Calculate coulomb interactions using cutoff
rcoulomb      = 0.0     ; Coulomb cutoff of infinity
vdw_type      = cut-off ; Calculate van der Waals interactions using cutoff
rvdw          = 0.0     ; Van der Waals cutoff of infinity
rlist         = 0.0     ; Neighbor list cutoff
nstlist       = 0       ; Do not update neighbor list
ns-type       = simple

implicit_solvent = GBSA ; Generalized Born implicit solvent
gb_algorithm     = HCT  ; Hawkins-Cramer-Truhlar radii calculation
rgbradii         = 0.0  ; Cutoff for Born radii calculation (A)
gb-saltconc      = 0.2  ; Salt concentration in M for Generalized Born 
models