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

[Daniel Adriano Silva M]

Mark,

Your are right. Thanks

Daniel

2009/9/24 Mark Abraham <Mark.Abraham at anu.edu.au>:
> 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.
>
> Mark
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>