[gmx-users] Domain decomposition error with implicit solvent

[Sapna Sarupria]

Dear All,

I am running simulations of BMP2 protein and graphite sheet using
implicit solvent model (mdp file is pasted below). The graphite atoms
are frozen in the simulation and BMP2 is free to translate.
I got an error "Step 1786210: The domain decomposition grid has
shifted too much in the Z-direction around cell 0 0 0" after 1749.7 ps
of the simulation.

I then restarted the simulation without changing anything using the
cpt file created from the previous (crashed) run and the simulation
continues. It has run for over 60 ps now and is continuing to run.
This is something we tried based on a previous email on gmxlist from
David van der Spoel. We are using gromacs 4.5.5.

Any idea what this error may be due to? We know that the system is not
blowing up since it continues to run with the cpt file.

Thanks,
Sapna

#### Start MDP file ############

dt                  =  0.001                    ; time step
nsteps              =  5000000                  ; number of steps
;nstcomm             =  10                      ; reset c.o.m. motion
nstxout             =  10                       ; write coords
nstvout             =  10                       ; write velocities
nstlog              =  10                       ; print to logfile
nstenergy           =  10                       ; print energies
xtc_grps            =  System
nstxtcout           =  10
nstlist             =  10                       ; update pairlist
ns_type             =  grid                     ; pairlist method
pbc                 =  no
rlist               =  1.5
rcoulomb            =  1.5
rvdw                =  1.5
implicit-solvent    =  GBSA
sa-algorithm        =  Ace-approximation
gb_algorithm        =  OBC
rgbradii            =  1.5
gb-epsilon-solvent  =  78.3
Tcoupl              =  V-rescale
ref_t               =  300.0
tc-grps             =  System
tau_t               =  0.5
gen_vel             =  yes                      ; generate init. vel
gen_temp            =  300                      ; init. temp.
gen_seed            =  372340                   ; random seed
;constraints         =  all-bonds                ; constraining bonds with H
;constraint_algorithm = lincs
refcoord-scaling    =  all
comm_mode           = ANGULAR
freezegrps          = Graphite
freezedim           = Y Y Y

#### End MDP file ############

-- 
Sapna Sarupria
Assistant Professor
Department of Chemical and
Biomolecular Engineering
128 Earle Hall
Clemson University
Clemson, SC 29634