[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
> > 
> >     ========================================
> >     _______________________________________________
> >     gmx-users mailing list    gmx-users at gromacs.org
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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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