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 <jalem...@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 <jalem...@vt.edu <mailto: >> 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> >> >> <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> >> > >> >> ==============================**__========== >> >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> >> <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> >> >> >> <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 >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> > -- > ==============================**========== > > 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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