[gmx-users] Domain Decomposition error with Implicit Solvent
mark.j.abraham at gmail.com
Wed Jul 23 22:20:41 CEST 2014
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
> 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.
> We know that the system is not blowing up since it continues to run with
> the cpt file.
> #### 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
> ;constraint_algorithm = lincs
> refcoord-scaling = all
> comm_mode = ANGULAR
> freezegrps = Graphite
> freezedim = Y Y Y
> #### End MDP file ############
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