hi justin ı used this mdp. file ..simulation box may be wrong.?..ı used dodecahedron distance edge 2.0 nm.....
; 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 <jalem...@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@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 | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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