<br /><br /><span>On 16/03/11, <b class="name">Moeed </b> <lecielll@googlemail.com> wrote:</span><blockquote cite="mid:AANLkTik0J4mYAHtUXMsGX-ZjRxmCFEL9-crFUiAzu_c9@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html">Dear experts,<br /><br />I am trying to build up a polymer in hexane system by increasing the density.</div></blockquote><br />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?<br /><br />Mark<br /><blockquote cite="mid:AANLkTik0J4mYAHtUXMsGX-ZjRxmCFEL9-crFUiAzu_c9@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"> 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 />
</div></blockquote>