[gmx-users] Error"Box was shifted at least 10 times. Please see log-file"
Justin A. Lemkul
jalemkul at vt.edu
Fri Oct 17 13:57:34 CEST 2008
There are several potential problems all combined into one. As has been
reported on the list, applying freezegrps, constraints, and pressure coupling
all at the same time do not mix well. The best bet is to turn off the pressure
coupling if you're set on using freezegrps. Otherwise, use position restraints
if you require NPT.
-Justin
vivek sharma wrote:
> 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 <mailto: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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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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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