[gmx-users] Error"Box was shifted at least 10 times. Please see log-file"
Berk Hess
gmx3 at hotmail.com
Fri Oct 17 14:48:12 CEST 2008
Hi,
In 3.3 position restraints and NPT can also cause trouble when the amount of scaling is large.
In 4.0 there is the new refcoord_scaling option that allows scaling
of the position restraint reference coordinates or their COM.
We would also like to have such a scaling for frozen atoms,
but that is not implemented yet.
Berk
> Date: Fri, 17 Oct 2008 07:57:34 -0400
> From: jalemkul at vt.edu
> To: viveksharma.iitb at gmail.com
> Subject: Re: [gmx-users] Error"Box was shifted at least 10 times. Please see log-file"
> CC: gmx-users at gromacs.org
>
> 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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