Dear experts,<br><br>I am trying to build up a polymer in hexane system by increasing the density. 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 <br>
<br>trjconv -s .tpr -f .trr -o frame2300.gro -dump 2300<br><br>to extract one of the frames before crash I did another NVT to equilibrate. <br>mpirun -np 4 mdrun_mpi -deffnm PE60-110Hex-NPT3-frame2300_md -s -o -c -g -e -x -v -pd <br>
<br>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.<br>
<br>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. <br><br>Moeed<br>===========================================<br>
<br>step 449800, will finish Tue Mar 15 11:23:55 2011<br>step 449900, will finish Tue Mar 15 11:23:55 2011<br>[node5:09563] *** Process received signal ***<br>[node5:09563] Signal: Segmentation fault (11)<br>[node5:09563] Signal code: Address not mapped (1)<br>
[node5:09563] Failing at address: 0xffffffff80849dc0<br>[node5:09563] [ 0] /lib64/libpthread.so.0 [0x3a2660eb10]<br>[node5:09563] [ 1] mdrun_mpi [0x4f0155]<br>[node5:09563] [ 2] mdrun_mpi(gmx_pme_do+0x216d) [0x4f9c1d]<br>
[node5:09563] [ 3] mdrun_mpi(do_force_lowlevel+0x21c8) [0x49c658]<br>[node5:09563] [ 4] mdrun_mpi(do_force+0xc59) [0x50db19]<br>[node5:09563] [ 5] mdrun_mpi(do_md+0x5623) [0x43e353]<br>[node5:09563] [ 6] mdrun_mpi(mdrunner+0xa07) [0x435e07]<br>
[node5:09563] [ 7] mdrun_mpi(main+0x1269) [0x443319]<br>[node5:09563] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3a25e1d994]<br>[node5:09563] [ 9] mdrun_mpi [0x420449]<br>[node5:09563] *** End of error message ***<br>
--------------------------------------------------------------------------<br>mpirun noticed that process rank 0 with PID 9563 on node node5.reyclus.loc exited on signal 11 (Segmentation fault).<br>-----------------------------------------------------------------------<br>
<br><br><br>pbc = xyz <br>;energygrps = PE HEX<br> <br>; Run control <br>integrator = md <br>dt = 0.002 <br>
nsteps = 1000000 ;5000 <br>nstcomm = 100 <br><br>; Output control<br>nstenergy = 100 <br>nstxout = 100 <br>nstvout = 0<br>
nstfout = 0<br>nstlog = 1000 <br>nstxtcout = 1000 <br><br>; Neighbor searching<br>nstlist = 10 <br>ns_type = grid <br>
<br>; Electrostatics/VdW <br>coulombtype = PME <br>vdw-type = Shift <br>rcoulomb-switch = 0 <br>rvdw-switch = 0.9 ;0 <br>
<br>; Cut-offs<br>rlist = 1.25 <br>rcoulomb = 1.25 ;1.1 <br>rvdw = 1.0 <br><br>; PME parameters<br>fourierspacing = 0.12 <br>
fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4 <br>ewald_rtol = 1e-5<br>optimize_fft = yes<br><br>; Temperature coupling <br>
Tcoupl = v-rescale <br>tc-grps = System ;HEX <br>tau_t = 0.1 ;0.1 <br>ref_t = 300 ;300 <br> <br>; Pressure coupling<br>
Pcoupl = no;berendsen <br>Pcoupltype = isotropic <br>tau_p = 0.5 ;0.5 <br>compressibility = 4.5e-5 4.5e-5 <br>ref_p = 30 30 <br>
<br>; Velocity generation <br>gen_vel = yes <br>gen_temp = 300.0 <br>gen_seed = 173529 <br><br>; Bonds<br>constraints = all-bonds <br>
constraint-algorithm = lincs<br><br>