Dear experts, I have been trying to do NVT on a system (a single polyethylene chain in 110 hexane) in the past few days but still no success. For some reason simulations are taking much longer than before. A run that used to complete in a few hours is taking several weeks. I am wondering if there is something wrong with our cluster or..my runs crash (LINCS) at early stages of simulation.
step 100, will finish Wed Mar 16 00:08:53 2011 step 200, will finish Wed Mar 16 00:05:57 2011 step 300, will finish Wed Mar 16 00:04:05 2011 step 400, will finish Wed Mar 16 00:03:37 2011 Step 460, time 0.92 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 22.298270, max 137.226395 (between atoms 2136 and 2138) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2123 2124 92.6 0.1090 0.1866 0.1090 2139 2142 90.0 0.1090 9.1450 0.1090 2139 2141 90.1 0.1090 9.2416 0.1090 2139 2140 90.0 0.1090 9.1782 0.1090 *********************************************************** Here is more details: To diagnose the reason for crash I watched the trajectory and noticed the problem lies in hexane molecules and not the polymer. All LINCS and 1-4 warnings are because of hexane. So I followed the instruction on gmx site and simplified the problem. Topology is not the root cause since a 2 ns run on a single hexane works well. I am not getting any warnings before MD step so be ignored by maxwarn either. Regarding bad intial structure I should say that I was initially using emtol= 1000 and then I used 100 and the box is too big and molecules are far apart. (box is 20nm containing 110 hexane) I also did PR where no error message come up. As I move on to MD NVT systems shows instabilities. I dont know how else to overcome this situation which I have been working on nearly one week. pbc = xyz ;energygrps = PE HEX ; Run control integrator = md dt = 0.002 nsteps = 1000000 ;5000 nstcomm = 100 ; Output control nstenergy = 100 nstxout = 1 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 1000 ; Neighbor searching nstlist = 10 ns_type = grid ; Electrostatics/VdW coulombtype = PME vdw-type = Shift rcoulomb-switch = 0 rvdw-switch = 0.9 ;0 ; Cut-offs rlist = 1.25 rcoulomb = 1.25 ;1.1 rvdw = 1.0 ; PME parameters fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Temperature coupling Tcoupl = v-rescale tc-grps = System ;HEX tau_t = 0.1 ;0.1 ref_t = 300 ;300 ; Pressure coupling Pcoupl = no;Parrinello-Rahman Pcoupltype = isotropic tau_p = 1 1 ;0.5 compressibility = 4.5e-5 4.5e-5 ref_p = 20 20 ; Velocity generation gen_vel = yes gen_temp = 300.0 gen_seed = 173529 ; Bonds constraints = all-bonds ; constraint-algorithm = lincs ; Free energy control stuff free_energy = no;yes init_lambda = 0 delta_lambda = 0 sc_alpha = 0.5 sc-power = 1 sc_sigma = 0.3 ;foreign_lambda = 0.1 dhdl_derivatives = yes ;couple-moltype = Polymer couple-lambda0 = vdw-q ;vdw couple-lambda1 = none ;vdw;none couple-intramol = yes nstdhdl = 10 separate_dhdl_file = yes dh_hist_size = 0 dh_hist_spacing = 0.1 > > Moeed wrote: > >> Hello Justin, >> >> I just scanned through the manual and also looked into the list to learn >> about the significance of reciprocal part to realize your statement. I did >> not find much about the fact that how I can judge if fourierspacing is the >> cause of the crash (I mean relevance between fourierspacing and coulb >> recip). I suspect the cause of crashes is because of >> > > The manual will not describe every detail, but an understanding of the > algorithms (through reading the appropriate literature) should provide you > with what you need. Take Mark's advice and leave fourierspacing at its > default value unless you are 100% sure of the effects of messing with it. > > > electrostatics settings. BEfore that I had only vdw no run crashed. >> > > That was a broken model, as we've discussed. Don't believe that its > results are reliable. > > > Since I used to get LINCS warning I removed bond constraints but still >> > > LINCS warnings don't mean you should turn off constraints. With a 2-fs > timestep and an all-atom model, you absolutely need to be using constraints. > > http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings > > > system is showing instabilities. I am confident that topology is fine and >> just wondering how else one can inspect root cause for unphysical forces. >> >> > The best advice I can give has already been given: > > > http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System > > Watch the trajectory. See what falls apart. > > You're also applying 70 bar of pressure to a system that may not yet be > properly equilibrated for such conditions. I have found that the > Parrinello-Rahman barostat is not particularly well-suited to harsh > conditions, tight coupling, or simulations of any system that is far from > equilibrium. You might be better off with Berendsen (and a fairly long > tau_p) until your system stabilizes. > > -Justin > > >> fourierspacing =0.12 : Coul. recip. 636.217 8.69433 >> 8.62908 0.0167398 3.68278 >> >> fourierspacing =0.3 : Coul. recip. 642.921 6.06063 >> 6.02832 -0.00984063 -2.16496 >> >> >> >> >> >> Everything has a cause; nothing is accidental. No stable run should >> ever show LINCS warnings like this, so yes, there is something to fix. >> >> You also have not proven that your fourierspacing is not the cause. >> The proper term to analyze is Coul-recip, which corresponds to >> reciprocal space Coulombic term. I don't see that listed below. >> >> -Justin >> >> >> Thanks, >> Best, >> Moeed >> >> ======================================== >> step 164300, remaining runtime: 241 s step 164400, >> remaining runtime: 240 s step 164500, remaining >> runtime: 240 s step 164600, remaining runtime: 239 >> s Warning: 1-4 interaction between 260 and 267 at >> distance 73679654.990 which is larger than the 1-4 table size >> 2.250 nm >> These are ignored for the rest of the simulation >> This usually means your system is exploding, >> if not, you should increase table-extension in your mdp file >> or with user tables increase the table size >> ========================================= >> results till t=320 ps (before first run crash) >> fourierspacing = 0.12 >> >> LJ-14 757.246 26.6239 26.5661 >> -0.0189929 -6.07777 >> >> Coulomb-14 -186.509 15.9866 15.9529 >> -0.0112174 -3.5896 >> >> LJ (SR) -2691.84 117.026 107.231 >> -0.507373 -162.361 >> >> Coulomb (SR) 725.662 17.6483 17.5876 >> 0.0158275 5.06483 >> >> fourierspacing = 0.3 >> >> >> LJ-14 757.129 26.4936 26.4578 >> -0.0149128 -4.77214 >> >> Coulomb-14 -199.523 14.949 14.158 >> -0.0519427 -16.6218 >> >> LJ (SR) -2670.5 111.201 109.688 >> 0.19784 63.3092 >> >> Coulomb (SR) 739.794 16.1807 15.4473 >> 0.0521352 16.6834 >> >> ==================================================== >> pbc = xyz ; Run >> control integrator = md >> dt = 0.002 nsteps = >> 1000000 ;5000 nstcomm = 100 >> ; Output control >> nstenergy = 100 nstxout >> = 100 nstvout = 0 >> nstfout = 0 >> nstlog = 1000 nstxtcout = >> 1000 ; Neighbor searching >> nstlist = 10 ns_type = >> grid ; Electrostatics/VdW >> coulombtype = PME vdw-type >> = Shift rcoulomb-switch = 0 >> rvdw-switch = 0.9 ;0 ; Cut-offs >> rlist = 1.25 rcoulomb >> = 1.25 ;1.1 rvdw = 1.0 >> ; PME parameters >> fourierspacing = 0.3 fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> pme_order = 4 ewald_rtol = 1e-5 >> optimize_fft = yes >> >> ; Temperature coupling Tcoupl = v-rescale >> tc-grps = System ;HEX >> tau_t = 0.1 ;0.1 ref_t >> = 400 ;300 ; Pressure coupling >> Pcoupl = Parrinello-Rahman Pcoupltype >> = isotropic tau_p = 1 >> 1 ;0.5 compressibility = 4.5e-5 4.5e-5 >> ref_p = 70 70 ; >> Velocity generation gen_vel = >> yes gen_temp = 300.0 >> gen_seed = 173529 ; Bonds >> constraints = all-bonds >> constraint-algorithm = lincs >> >> >> -- ======================================== >> >> 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 >> >> 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 >> Please search the archive at >> 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-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- >> Moeed Shahamat >> Graduate Student (Materials Modeling Research Group) >> McGill University- Department of Chemical Engineering >> Montreal, Quebec H3A 2B2, Canada >> Web: >> http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php >> Web:http://mmrg.chemeng.mcgill.ca/ >> >> > -- > ======================================== > > 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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > 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 >
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