On 16/03/11, Moeed <lecie...@googlemail.com> wrote: > Dear experts, > > I am trying to build up a polymer in hexane system by increasing the density. >
This seems to have been taking months. Why aren't you using genbox on your polymer starting configuration and an equilibrated box of hexane of the right density? Mark > 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 I did another NVT to equilibrate. > mpirun -np 4 mdrun_mpi -deffnm PE60-110Hex-NPT3-frame2300_md -s -o -c -g -e > -x -v -pd > > > 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. Please help me with this. Thank you > in advance. > > > more details: There is only one polyethylene chain ( 60 units) in 110 hexane. > The chain is not convoluted and has a little extended shape, which make it > not easy fit in the box. > > 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 > ;energygrps = PE HEX > > ; 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 > > > >
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