[gmx-users] segmantation default
Justin A. Lemkul
jalemkul at vt.edu
Thu Feb 2 16:03:03 CET 2012
mehmet kıytak wrote:
> hi Justin... you were right.. my equilibration is ınsufficient...ı
> increase nsteps 50000....200000..now ı recieve this message..
>
> Fatal error:
> The Z-size of the box (1.957000) times the triclinic skew factor
> (1.000000) is smaller than the number of DD cells (2) times the smallest
> allowed cell size (1.000000)
>
> How can ı solve this problem...please help me...
>
The error is still symptomatic of a crash. Your box is distorting too much and
various algorithms (most notably DD) are crashing.
-Justin
> 1 Şubat 2012 22:37 tarihinde Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> yazdı:
>
>
>
> mehmet kıytak wrote:
>
> hi justin
> ı used this mdp. file ..simulation box may be wrong.?..ı used
> dodecahedron distance edge 2.0 nm.....
>
>
> No, that's almost certainly not the problem. Insufficient
> minimization/equilibration, or instability due to the use of the
> free energy code is more likely. You look to be trying to decouple
> the entire system, which could be an unstable process. You haven't
> said what you're doing, so I won't hazard a guess at this point.
> Please refer to the link I provided and try running without the
> free energy code. Otherwise, you're (potentially) trying to solve
> several problems at once.
>
> -Justin
>
> ; Run control
> integrator = sd ; Langevin dynamics
> tinit = 0
> dt = 0.002
> nsteps = 2500000 ; 5 ns
> nstcomm = 100
> ; Output control
> nstxout = 0
> nstvout = 0
> nstfout = 0
> nstlog = 0
> nstenergy = 0
> nstxtcout = 0
> xtc-precision = 1000
> ; Neighborsearching and short-range nonbonded interactions
> nstlist = 10
> ns_type = grid
> pbc = xyz
> rlist = 1.0
> ; Electrostatics
> coulombtype = PME
> rcoulomb = 1.0
> ; van der Waals
> vdw-type = switch
> rvdw-switch = 0.8
> rvdw = 0.9
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = EnerPres
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing = 0.12
> ; EWALD/PME/PPPM parameters
> pme_order = 6
> ewald_rtol = 1e-06
> epsilon_surface = 0
> optimize_fft = no
> ; Temperature coupling
> ; tcoupl is implicitly handled by the sd integrator
> tc_grps = system
> tau_t = 1.0
> ref_t = 300
> ; Pressure coupling is on for NPT
> Pcoupl = Parrinello-Rahman
> tau_p = 0.5
> compressibility = 4.5e-05
> ref_p = 1.0
> ; Free energy control stuff
> free_energy = yes
> init_lambda = 0.0
> delta_lambda = 0
> foreign_lambda = 0.05
> sc-alpha = 0.5
> sc-power = 1.0
> sc-sigma = 0.3
> couple-moltype = system ; name of moleculetype to
> decouple
> couple-lambda0 = vdw ; only van der Waals
> interactions
> couple-lambda1 = none ; turn off everything, in
> this case only vdW
> couple-intramol = no
> nstdhdl = 10
> ; Do not generate velocities
> gen_vel = no
> ; options for bonds
> constraints = h-bonds ; we only have C-H bonds here
> ; Type of constraint algorithm
> constraint-algorithm = lincs
> ; Constrain the starting configuration
> ; since we are continuing from NPT
> continuation = yes
> ; Highest order in the expansion of the constraint coupling matrix
> lincs-order = 12
>
>
> 1 Şubat 2012 19:41 tarihinde Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>>> yazdı:
>
>
>
>
> mehmet kıytak wrote:
>
> hi all...
> ı have a problem.. ı got segmentation fault when run nvt
> equilibration.. ı use below mdp file
>
>
> Please post a complete .mdp file. The Unix 'cat' command can be
> used to print the contents of the text file, which can then be
> copied and pasted into an email.
>
>
>
> couple-lambda0 = vdw ; only van der Waals
> interactions
> couple-lambda1 = none ; turn off everything, in
> this case only vdW
> couple-intramol = no
> nstdhdl = 10
>
>
> It appears you are trying to do a free energy calculation by
> transforming your system. Turn off the free energy code to
> determine whether or not this is a source of the problem.
>
> <snip>
>
>
> Step 3, time 0.006 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.337002, max 0.559171 (between atoms 1 and 4)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 1 2 90.0 0.1006 0.1091 0.1000
> 1 3 90.0 0.2058 0.1141 0.1000
> 1 4 90.0 0.3028 0.1559 0.1000
>
> Back Off! I just backed up step3b_n3.pdb to
> ./#step3b_n3.pdb.1#
>
> Back Off! I just backed up step3b_n4.pdb to
> ./#step3b_n4.pdb.1#
>
> Back Off! I just backed up step3c_n2.pdb to
> ./#step3c_n2.pdb.1#
>
> Back Off! I just backed up step3c_n3.pdb to
> ./#step3c_n3.pdb.1#
>
> Back Off! I just backed up step3c_n4.pdb to
> ./#step3c_n4.pdb.1#
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> Segmentation fault
> mkiytak at babil:~
>
> PLEASE HELP ME...
>
>
> LINCS warnings are the most common error reported to this list.
> Please refer to the following pages for help:
>
>
> http://www.gromacs.org/____Documentation/Errors#LINCS.____2fSETTLE.2fSHAKE_warnings
> <http://www.gromacs.org/__Documentation/Errors#LINCS.__2fSETTLE.2fSHAKE_warnings>
>
>
> <http://www.gromacs.org/__Documentation/Errors#LINCS.__2fSETTLE.2fSHAKE_warnings
> <http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings>>
>
> If you still can't find your answer, refer to the list
> archive. As
> I said, such errors are commonly reported. Surely you'll find
> something useful. The only thing that can be said right now
> is that
> your system is unstable. Either you need better minimization or
> equilibration (or both), your .mdp settings are incorrect, or the
> free energy code is causing an instability (which is a symptom of
> the first two points, it does not suggest the free energy code is
> not working).
>
> -Justin
>
> -- ==============================____==========
>
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
> 231-9080 <tel:%28540%29%20231-9080>
> <tel:%28540%29%20231-9080>
> http://www.bevanlab.biochem.____vt.edu/Pages/Personal/justin
> <http://vt.edu/Pages/Personal/justin>
> <http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>>
>
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> --
> ==============================__==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> <tel:%28540%29%20231-9080>
> http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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