[gmx-users] BUG in GROMACS 4.0.5, related to very log total integration time

[Berk Hess]

> Date: Fri, 25 Sep 2009 08:23:37 +1000
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] BUG in GROMACS 4.0.5,	related to very log total integration time
> 
> Daniel Adriano Silva M wrote:
> > Dear GROMACS users and developers.
> > 
> > I don known if this issued had been previously addressed, but I found
> > that when I try to run a MD with time-step of 2fs and 2500000000 steps
> > (yes 500us!!!) the dynamics aborts with the next message (64bit-LINUX
> > and icc 10 compiler):
> > 
> > ####################
> > WARNING: This run will generate roughly 20576946697451257856 Mb of data
> > 
> > starting mdrun 'F1-ATPASE'
> > -1794967296 steps, -3589934.8 ps.
> > 
> > nodetime = 0! Infinite Giga flopses!
> >         Parallel run - timing based on wallclock.
> > 
> > #####################
> > 
> > If i reduce the steps number by one order of magnitude then all goes
> > ok.  My MDP when I obtined this error was:
> > 
> > 
> > ; VARIOUS PREPROCESSING OPTIONS
> > title                    = NPT simulacion
> > cpp                      = /lib/cpp
> > 
> > ; RUN CONTROL PARAMETERS
> > integrator               = md
> > dt                       = 0.002
> > nsteps                   = 2500000000
> > nstxout                  = 5000
> > nstvout                  = 5000
> > nstlog                   = 2500
> > nstenergy                = 2500
> > nstxtcout                = 2500
> > energygrps               = Protein Non-Protein
> > nstlist         = 10
> > rlist           = 1.0
> > ns_type         = grid
> > pbc             = xyz
> > coulombtype              = pme
> > rcoulomb                 = 1.0
> > vdw-type                 = Cut-off
> > rvdw                     = 1.0
> > fourierspacing       =  0.12
> > pme_order            =  4
> > optimize_fft         =  yes
> > ewald_rtol           =  1e-5
> > tcoupl                   = Berendsen
> > tc-grps                  = Protein  Non-Protein
> > tau_t                    = 0.1      0.1
> > ref_t                    = 300      300
> > Pcoupl                   = Parrinello-Rahman
> > Pcoupltype               = Isotropic
> > tau_p                    = 1.0
> > ref_p                    = 1.0
> > compressibility          = 4.5e-5
> > gen_vel                  = no
> > constraints              = all-bonds
> > constraint-algorithm     = Lincs
> > unconstrained-start      = yes
> > lincs-order              = 4
> > lincs-iter               = 1
> > lincs-warnangle          = 30
> > 
> > I known this kind of error is not a priority since the total
> > integration time is ridiculous big, but anyway I want to comment it to
> > you.
> 
> Yes, it's known. IIRC there was some discussion on the developers list 
> about changing the relevant data type so that it can store bigger 
> numbers. It's also a non-problem inasmuch as if you are ever able to run 
> a simulation that long, manually resetting the number of steps to zero 
> at a suitable point will be workable.

This issue has already been fixed for the 4.1 release.

Berk

 		 	   		  
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