[gmx-users] segmantation default
mehmet kıytak
mehmetkiytak at gmail.com
Thu Feb 2 16:01:43 CET 2012
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...
1 Şubat 2012 22:37 tarihinde Justin A. Lemkul <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>> 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> | (540) 231-9080
>> <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 | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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