[gmx-users] Error"Box was shifted at least 10 times. Please see log-file"

[vivek sharma]

Hi justin,

thanks for your response.....
following is the .mdp file pasted..

_____
title               = trp_drg
warnings            = 10
cpp                 = /lib/cpp ; location of cpp on SGI
define              = -DPOSRES
constraints         = all-bonds
integrator          = md
dt                  = 0.002 ; ps !
nsteps              = 2500000 ; total 5000.0 ps.
nstcomm             = 1
nstxout             = 25000 ; output coordinates every 0.5 ps
nstvout             = 100000 ; output velocities every 2.0 ps
nstfout             = 0
nstlog              = 10
nstenergy           = 10
nstlist             = 10
ns_type             = grid
rlist               = 0.9
coulombtype         = PME
rcoulomb            = 0.9
rvdw                = 1.0
energygrps_excl     = freeze freeze freeze SOL  ! To remove
computation of interactions between the frozen groups with
surroundings (i.e. the solvent, SOL)

fourierspacing      = 0.12
fourier_nx          = 0
fourier_ny          = 0
fourier_nz          = 0
pme_order           = 6
ewald_rtol          = 1e-5
optimize_fft        = yes
; Berendsen temperature coupling is on in four groups
Tcoupl              = berendsen
tau_t               = 0.1        0.1   0.1
tc_grps             = protein    sol   NDP
ref_t               = 300        300   300
; Pressure coupling is on
Pcoupl              = berendsen
pcoupltype          = isotropic
tau_p               = 0.5
compressibility     = 4.5e-5
ref_p               = 1.0
; Generate velocites is on at 300 K.
gen_vel             = yes
gen_temp            = 300.0
gen_seed            = 173529
; Non-equilibrium MD stuff
freezegrps               = freeze
freezedim                = Y Y Y
____

With Thanks,
Vivek

2008/10/17 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> vivek sharma wrote:
>
>> Hi Tehre,
>> i am running a job by keeping a part of molecule freeze ....by using the
>> .mdp option....
>>
>
> What is your entire .mdp file?
>
> -Justin
>
>  ______________
>>
> ________
>
>> energygrps_excl        =  Terminal Terminal Terminal SOL  ! To remove
>> computation of nonbonding interactions between the frozen groups with each
>> other
>> and surroundings (i.e. the solvent, SOL)
>> freezegrps              =  Terminal  ! Index group to freeze
>> freezedim               =  Y Y Y     ! Freeze this group in all
>> directions, x,
>> y, and z
>> ___________________________________________________
>>
>>
>> where frreze is a group mentioned in the index file...
>> During the run the job is being terminated with the following error
>> .
>> __________________________________________________________
>> Step 1  Warning: pressure scaling more than 1%, mu: -3.51079e+22
>> -3.51079e+22 -3.51079e+22
>>
>> -------------------------------------------------------
>> Program mdrun_d, VERSION 3.3.3
>> Source code file: ns.c, line: 258
>>
>> Fatal error:
>> Box was shifted at least 10 times. Please see log-file.
>> -------------------------------------------------------
>>
>> Error on node 0, will try to stop all the nodes
>> Halting parallel program mdrun_d on CPU 0 out of 24
>>
>> srun: error: n216: task0: Aborted
>> srun: Terminating job
>> __________________________________________________________________
>>
>> Can somebody give an insight in the problem for figuring out the probable
>> cause of the error.
>>
>> PS::Before the run I mentioned the boxsize in editconf as "-box 7.5 5 6 ",
>> to keep the size of box and number of solvent optimum.
>> Does it have anything to do with the mentioned error ?
>>
>>
>> Looking for suggestions..
>>  with thanks,
>> Vivek
>>
>>
>> ------------------------------------------------------------------------
>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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