[gmx-users] Domain Decomposition error with Implicit Solvent

[Mark Abraham]

On Mon, Jul 21, 2014 at 3:48 PM, Siva Dasetty <sdasett at g.clemson.edu> wrote:

> 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?


Could be anything. I have a hundred bucks that says no developer has ever
run with frozen groups and implicit solvent. :-) Consider yourself warned!
However, you should look at the trajectory as it approaches the failing
step to see what the trigger is - e.g. diffusion further away than the
sheet is wide, or something.

Mark


> We know that the system is not blowing up since it continues to run with
> the cpt file.
>
> Thanks,
> Siva
>
> #### 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 ############
> --
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