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. **************************************** 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: *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
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