[gmx-users] Potassium channel EM Segmentation fault

[Vytautas Rakeviius]

I suggest ignoring/deleting TL and then replacing waters with K randomly with:gmx genion.Ofc. it depends what you try to do.
 

    On Wednesday, October 11, 2017, 5:01:52 PM GMT+3, Du, Yu <duyu at sioc.ac.cn> wrote:  
 
 Dear GMX Users, 


Keyword: metal, energy minimization, segmentation fault 


I have pinpointed the source of EM error. EM succeeds only without potassiums. 


I used PDB 1r3j and changed the TL to K.
You can download the my 1r3j here and reproduce the error like this.


$gmx pdb2gmx -f 1r3j_kchannel.pdb -o 1r3j.gro -ignh -water tip3p
$gmx grompp -f minim.mdp -c 1r3j.gro -p topol.top -o em.tpr
$mpirun -np 20 gmx_mpi mdrun -ntomp 1 -s em.tpr


Thanks for any solutions.


######################The minim.mdp file######################
define=-DPOSRES
; Parameters describing what to do, when to stop and what to save
integrator  = steep    ; Algorithm (steep = steepest descent minimization)
emtol      = 1000.0    ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep      = 0.01      ; Energy step size
nsteps      = 50000    ; Maximum number of (minimization) steps to perform


; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist    = 1        ; Frequency to update the neighbor list and long range forces
cutoff-scheme = verlet
ns_type    = grid      ; Method to determine neighbor list (simple, grid)
rlist      = 1.2      ; Cut-off for making neighbor list (short range forces)
coulombtype = PME      ; Treatment of long range electrostatic interactions
rcoulomb    = 1.2      ; Short-range electrostatic cut-off
rvdw        = 1.2      ; Short-range Van der Waals cut-off
pbc        = xyz      ; Periodic Boundary Conditions
###################################END##########################


############################EM Error############################

Steepest Descents:
  Tolerance (Fmax)  =  1.00000e+03
  Number of steps    =        50000
[gpu-new:22930] *** Process received signal ***
[gpu-new:22930] Signal: Segmentation fault (11)
[gpu-new:22930] Signal code: Address not mapped (1)
[gpu-new:22930] Failing at address: 0xfffffffe01bf6dd0
[gpu-new:22930] [ 0] /lib64/libpthread.so.0[0x383660f710]
[gpu-new:22930] [ 1] /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(+0xe6c36f)[0x2b1966ebe36f]
[gpu-new:22930] [ 2] /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(+0xe6d65f)[0x2b1966ebf65f]
[gpu-new:22930] [ 3] /home/duyu/software/gcc-4.9.4/lib64/libgomp.so.1(GOMP_parallel+0x3f)[0x2b196d7a58cf]
[gpu-new:22930] [ 4] /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(_Z17nbnxn_put_on_gridP12nbnxn_searchiPA3_fiPfS3_iifPKiS2_iPiiP16nbnxn_atomdata_t+0xecd)[0x2b1966ec28fd]
[gpu-new:22930] [ 5] /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(dd_partition_system+0x2c67)[0x2b19661ed6b7]
[gpu-new:22930] [ 6] /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(+0xe0379d)[0x2b1966e5579d]
[gpu-new:22930] [ 7] /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(_ZN3gmx8do_steepEP8_IO_FILEP9t_commreciPK8t_filenmPK16gmx_output_env_tiiP11gmx_vsite_tP10gmx_constriP10t_inputrecP10gmx_mtop_tP8t_fcdataP7t_stateP9t_mdatomsP6t_nrnbP13gmx_wallcycleP9gmx_edsamP10t_forcereciiiP12gmx_membed_tffimP23gmx_walltime_accounting+0x353)[0x2b1966e69aa3]
[gpu-new:22930] [ 8] gmx_mpi(_ZN3gmx8mdrunnerEP12gmx_hw_opt_tP8_IO_FILEP9t_commreciPK8t_filenmPK16gmx_output_env_tiiPiiiffPKcfSE_SE_SE_SE_iliiiiiifffim+0x190a)[0x4101ca]
[gpu-new:22930] [ 9] gmx_mpi(_Z9gmx_mdruniPPc+0x1766)[0x421516]
[gpu-new:22930] [10] /home/duyu/software/gromacs-2016.3p2.3/lib64/libgromacs_mpi.so.2(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x2a3)[0x2b19661a5693]
[gpu-new:22930] [11] gmx_mpi(main+0x7c)[0x40cd3c]
[gpu-new:22930] [12] /lib64/libc.so.6(__libc_start_main+0xfd)[0x383621ed1d]
[gpu-new:22930] [13] gmx_mpi[0x40cb79]
[gpu-new:22930] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 0 on node gpu-new exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
###################################END##########################


--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275
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