On 20 March 2011 15:23, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Moeed wrote: > >> Dear experts, >> >> I am trying to build up a polymer in hexane system by increasing the >> density and use this for FE calculation. After PR step, my NVT and NPT >> trailes failed. Initially I used to get LINCS and 1-4 warnings (even for >> NVT) which were not because of flawed topology file. It turned out that >> simulations crashed just because of using -np > 4. But still even with this >> -np, NPT did not work which made me to swtich to berendsen from parrinelo >> rahman scheme. As I approched the desired density again simulation crashed, >> so I used >> >> trjconv -s .tpr -f .trr -o frame2300.gro -dump 2300 >> >> to extract one of the frames before crash then I did another NVT to >> equilibrate. >> mpirun -np 4 mdrun_mpi -deffnm PE60-110Hex-NPT-frame2300_md >> >> after around 1 ns I get the error below ( mdp file is also included). I >> described above since I encountered the situation where root cause of >> problem was not topology and just the computational issue ( I mean -np), I >> am just curious if the same thing applies here. So I have two concerns: >> >> 1- Crash at the early stages of run ( topology is working fine for a >> single hexane, so this can not be the reason). only works only for -np =<4. >> >> 2- Crash when compressing because chain crashes on itself. ( I have no >> control on this because chains takes different shapes and becomes extended) >> >> >> can you please comment on the proper settings for compressing the system. >> >> more details: There is only one polyethylene chain ( 60 units) in 110 >> hexane ( box size 20 nm at the beginning) The chain is not convoluted and >> has a little extended shape that crashes on itself for long runs. >> >> > This is likely the problem. The compression of the system is occurring too > fast for the system to adequately respond. If the PE chain is fully > extended, any significant change in the box size (which is mostly a function > of the solvent, in this case, hexane) will case PE to interact via PBC and > collapse. > > > **************************************** >> Mark: Why aren't you using genbox on your polymer starting configuration >> and an equilibrated box of hexane of the right density? >> >> me: Hi, I need to work with polymer 15 Wt% system, so I manually >> calculated how many hexane I need to get this concentration. So for a single >> PE chain of 60 units I need 110 hexane. Here is the command: >> >> > The treatment of your system is also problematic. You need a certain > composition, but a straight PE chain with only 110 hexane will probably > respond very drastically to any non-equilibrium conditions. You need to > generate a more sensible configuration for the PE chain such that it does > not collide with itself. I would suspect that a more compact PE chain in > conjunction with a hexane box with a density closer to your target would (1) > eliminate the need for compression and (2) be more stable. >
Thank you. 1- So You mean I should compress a chain separately and make a hexane box and combine these two? How is this possible to insert a solute in a prepared solvent box? 2- As I compress the system (NPT equilibrated to density of 0.62 g/l) chain takes a realistic shape, which is not extended. NVT on this configuration sometimes cause the chain to a more straight chain.Now I extracted a frame from NPT a little before equilibration (density 0.5, and actually this is the density I want) and equilibrated by NVT and no crash happened. As I asked in previous message I only want to assure if I can extract a frame ( even density is not equilibrated) followed by NVT to equilibbrate and use this as production runs.? > -Justin > > /genbox -cp PE60.gro -ci Hexane.gro -o PE60-110Hex.gro -nmol 110 / >> >> >> /since chains is completely extended ( ~ 16 nm) I am using a cubic box of >> 20 nm and add 110 hexane which gives a very low density./ >> >> // >> >> Can you please let me know how else genbox can be employed for this >> purpose>? ( if there is a better way of doing this) >> >> Also, If I compress to a density higher than needed, can I view the >> density profile and read off the time that gives the desired density and >> extract that frame ( with command above) followed by NVT to equilibrate and >> use that as prodcution run? >> >> Please help me with this. >> Thanks a lot, >> Moeed >> =========================================== >> >> step 449800, will finish Tue Mar 15 11:23:55 2011 >> step 449900, will finish Tue Mar 15 11:23:55 2011 >> [node5:09563] *** Process received signal *** >> [node5:09563] Signal: Segmentation fault (11) >> [node5:09563] Signal code: Address not mapped (1) >> [node5:09563] Failing at address: 0xffffffff80849dc0 >> [node5:09563] [ 0] /lib64/libpthread.so.0 [0x3a2660eb10] >> [node5:09563] [ 1] mdrun_mpi [0x4f0155] >> [node5:09563] [ 2] mdrun_mpi(gmx_pme_do+0x216d) [0x4f9c1d] >> [node5:09563] [ 3] mdrun_mpi(do_force_lowlevel+0x21c8) [0x49c658] >> [node5:09563] [ 4] mdrun_mpi(do_force+0xc59) [0x50db19] >> [node5:09563] [ 5] mdrun_mpi(do_md+0x5623) [0x43e353] >> [node5:09563] [ 6] mdrun_mpi(mdrunner+0xa07) [0x435e07] >> [node5:09563] [ 7] mdrun_mpi(main+0x1269) [0x443319] >> [node5:09563] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3a25e1d994] >> [node5:09563] [ 9] mdrun_mpi [0x420449] >> [node5:09563] *** End of error message *** >> -------------------------------------------------------------------------- >> mpirun noticed that process rank 0 with PID 9563 on node node5.reyclus.loc >> exited on signal 11 (Segmentation fault). >> ----------------------------------------------------------------------- >> >> >> >> 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 = 0.12 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;berendsen Pcoupltype = >> isotropic tau_p = 0.5 ;0.5 >> compressibility = 4.5e-5 4.5e-5 ref_p = 30 30 >> >> ; 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 | (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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