[gmx-users] segmantation default
Justin A. Lemkul
jalemkul at vt.edu
Wed Feb 1 21:37:31 CET 2012
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>
>
> 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://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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