[gmx-users] Domain Decomposition error with Implicit Solvent
sdasett at g.clemson.edu
Sun Jul 27 04:12:12 CEST 2014
Thank you Mark for the reply.
We are not sure about it either as it worked when we started the simulation again using the cpt file and also there
was no issue when we did the same simulation using (links algorithm) constraints.
On Jul 23, 2014, at 4:20 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 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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