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Hi everyone!
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<p>
I'm trying to run a simulation of a single diatomic Sulfur molecule. When I run an equilibration scheme (generating velocities from a 300K Maxwell-Boltzmann distribution) it runs fine, but when I take the equilibrated molecule and couple one atom to a 0K heat bath (using Stochastic Dynamics) the simulation segfaults at the first step.
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<p>
I've enclosed as much information as I could. Notice (at the very bottom) that the md.log file shows an initial temperature of 17884.7K, but already in the report for step 0 the temperature, as well as many other thermodynamic quantities, are NaN.
</p>
<p>
I've encountered one reference to the same error I'm getting, but itjust said that there was some problem with the input files, but didn'tsay what was the problem...
</p>
<p>
I hope you will find some stupid mistake in the *.mdp file, or something easily remedied...
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<p>
P.S.
</p>
<p>
I know GROMACS is not optimized for simulating tiny molecules, but I don't see why it should be such a critical problem...
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<p>
<br />
</p>
<p>
A wholotta supplemental data:
</p>
<p>
<br />
MDRUN_MPI STD-I/O:<br />
==================<br />
<br />
step 0<br />
[hydrogen:15285] *** Process received signal ***<br />
[hydrogen:15285] Signal: Segmentation fault (11)<br />
[hydrogen:15285] Signal code: Address not mapped (1)<br />
[hydrogen:15285] Failing at address: 0xfffffffe16c50a90<br />
[hydrogen:15285] [ 0] /lib64/libpthread.so.0 [0x355c00de80]<br />
[hydrogen:15285] [ 1] mdrun_mpi(gmx_pme_do+0x28b2) [0x4b56f2]<br />
[hydrogen:15285] [ 2] mdrun_mpi(do_force_lowlevel+0x1023) [0x47f6f3]<br />
[hydrogen:15285] [ 3] mdrun_mpi(do_force+0xe6e) [0x4c99ce]<br />
[hydrogen:15285] [ 4] mdrun_mpi(do_md+0x48f0) [0x42c4a0]<br />
[hydrogen:15285] [ 5] mdrun_mpi(mdrunner+0x831) [0x42d771]<br />
[hydrogen:15285] [ 6] mdrun_mpi(main+0x3c0) [0x42e6a0]<br />
[hydrogen:15285] [ 7] /lib64/libc.so.6(__libc_start_main+0xf4) [0x355b41d8b4]<br />
[hydrogen:15285] [ 8] mdrun_mpi [0x4131a9]<br />
[hydrogen:15285] *** End of error message ***<br />
./test-2-6-09.sh: line 16: 15285 Segmentation fault      mdrun_mpi -c md -v<br />
<br />
<br />
----------------------------------------------------------------------------------------------------------------<br />
<br />
MD.MDP<br />
======<br />
<br />
integrator    =    sd    ;stochastic dynamics (velocity Langevin) using a leap-frog algorithm<br />
dt        =    0.0001<br />
nsteps        =    10000                        ; [steps] ==> total (nsteps*dt) ps.<br />
nstxout        =    1<br />
nstvout        =    1<br />
nstfout        =    1<br />
; nstxtcout    =    1<br />
nstenergy    =    1    ; write energies to energy file every 1000 steps (default 100)<br />
nstlog        =    1<br />
energygrps    =    SL    SR<br />
ns_type            =    simple<br />
periodic_molecules    =    no<br />
coulombtype    =    PME<br />
tc-grps        =    SL    SR<br />
tau_t        =    0    1    ; mass/gamma<br />
ref_t        =    0       0    ; refference (bath) temperature<br />
Pcoupl        =    no<br />
gen_vel        =    no<br />
gen_seed    =    -1    ; random seed based on computer clock<br />
constraints    =    none<br />
<br />
--------------------------------------------------------------------------------------------<br />
<br />
1S2.itp<br />
=======<br />
<br />
[ atomtypes ]<br />
;atomtype     m (u)     q (e)    part.type     V(cr)    W(cr)<br />
SX        32.0600    0.000    A        1E-03    1E-05<br />
<br />
[ moleculetype ]<br />
; Name nrexcl<br />
1S2      2<br />
<br />
[ atoms ]<br />
;   nr    type  resnr resid  atom  cgnr   charge     mass<br />
    1      SX     1  1S2     SL     1    0.000  32.0600<br />
    2      SX     1  1S2     SR     2    0.000  32.0600<br />
<br />
[ bonds ]<br />
; ai  aj  fu    c0, c1, ...<br />
   1   2   2    0.2040  5.3E+6    0.2040  5.3E+6 ;   SL SR<br />
<br />
--------------------------------------------------------------------------------------------<br />
<br />
TRAJ.TRR<br />
========<br />
<br />
traj.trr frame 0:<br />
   natoms=         2  step=         0  time=0.0000000e+00  lambda=         0<br />
   box (3x3):<br />
      box[    0]={ 6.37511e+00,  0.00000e+00,  0.00000e+00}<br />
      box[    1]={ 0.00000e+00,  6.37511e+00,  0.00000e+00}<br />
      box[    2]={ 0.00000e+00,  0.00000e+00,  6.37511e+00}<br />
   x (2x3):<br />
      x[    0]={ 3.19756e+00,  3.20532e+00,  3.18725e+00}<br />
      x[    1]={ 3.03044e+00,  3.21568e+00,  3.08875e+00}<br />
   v (2x3):<br />
      v[    0]={ 2.22763e+00, -2.56083e-01,  1.38905e+00}<br />
      v[    1]={-2.22763e+00,  2.56083e-01, -1.38905e+00}<br />
   f (2x3):<br />
      f[    0]={ 3.43615e+03, -2.13216e+02,  2.02509e+03}<br />
      f[    1]={-3.43615e+03,  2.13216e+02, -2.02509e+03}<br />
<br />
<br />
--------------------------------------------------------------------------------------------<br />
<br />
MD.LOG<br />
======<br />
<br />
<br />
<br />
Input Parameters:<br />
   integrator           = sd<br />
   nsteps               = 10000<br />
   init_step            = 0<br />
   ns_type              = Simple<br />
   nstlist              = 10<br />
   ndelta               = 2<br />
   nstcomm              = 1<br />
   comm_mode            = Linear<br />
   nstlog               = 1<br />
   nstxout              = 1<br />
   nstvout              = 1<br />
   nstfout              = 1<br />
   nstenergy            = 1<br />
   nstxtcout            = 0<br />
   init_t               = 0<br />
   delta_t              = 0.0001<br />
   xtcprec              = 1000<br />
   nkx                  = 54<br />
   nky                  = 54<br />
   nkz                  = 54<br />
   pme_order            = 4<br />
   ewald_rtol           = 1e-05<br />
   ewald_geometry       = 0<br />
   epsilon_surface      = 0<br />
   optimize_fft         = FALSE<br />
   ePBC                 = xyz<br />
   bPeriodicMols        = FALSE<br />
   bContinuation        = FALSE<br />
   bShakeSOR            = FALSE<br />
   etc                  = No<br />
   epc                  = No<br />
   epctype              = Isotropic<br />
   tau_p                = 1<br />
   ref_p (3x3):<br />
      ref_p[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}<br />
      ref_p[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}<br />
      ref_p[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}<br />
   compress (3x3):<br />
      compress[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}<br />
      compress[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}<br />
      compress[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}<br />
   refcoord_scaling     = No<br />
   posres_com (3):<br />
      posres_com[0]= 0.00000e+00<br />
      posres_com[1]= 0.00000e+00<br />
      posres_com[2]= 0.00000e+00<br />
   posres_comB (3):<br />
      posres_comB[0]= 0.00000e+00<br />
      posres_comB[1]= 0.00000e+00<br />
      posres_comB[2]= 0.00000e+00<br />
   andersen_seed        = 815131<br />
   rlist                = 1<br />
   rtpi                 = 0.05<br />
   coulombtype          = PME<br />
   rcoulomb_switch      = 0<br />
   rcoulomb             = 1<br />
   vdwtype              = Cut-off<br />
   rvdw_switch          = 0<br />
   rvdw                 = 1<br />
   epsilon_r            = 1<br />
   epsilon_rf           = 1<br />
   tabext               = 1<br />
   implicit_solvent     = No<br />
   gb_algorithm         = Still<br />
   gb_epsilon_solvent   = 80<br />
   nstgbradii           = 1<br />
   rgbradii             = 2<br />
   gb_saltconc          = 0<br />
   gb_obc_alpha         = 1<br />
   gb_obc_beta          = 0.8<br />
   gb_obc_gamma         = 4.85<br />
   sa_surface_tension   = 2.092<br />
   DispCorr             = No<br />
   free_energy          = no<br />
   init_lambda          = 0<br />
   sc_alpha             = 0<br />
   sc_power             = 0<br />
   sc_sigma             = 0.3<br />
   delta_lambda         = 0<br />
   nwall                = 0<br />
   wall_type            = 9-3<br />
   wall_atomtype[0]     = -1<br />
   wall_atomtype[1]     = -1<br />
   wall_density[0]      = 0<br />
   wall_density[1]      = 0<br />
   wall_ewald_zfac      = 3<br />
   pull                 = no<br />
   disre                = No<br />
   disre_weighting      = Conservative<br />
   disre_mixed          = FALSE<br />
   dr_fc                = 1000<br />
   dr_tau               = 0<br />
   nstdisreout          = 100<br />
   orires_fc            = 0<br />
   orires_tau           = 0<br />
   nstorireout          = 100<br />
   dihre-fc             = 1000<br />
   em_stepsize          = 0.01<br />
   em_tol               = 10<br />
   niter                = 20<br />
   fc_stepsize          = 0<br />
   nstcgsteep           = 1000<br />
   nbfgscorr            = 10<br />
   ConstAlg             = Lincs<br />
   shake_tol            = 0.0001<br />
   lincs_order          = 4<br />
   lincs_warnangle      = 30<br />
   lincs_iter           = 1<br />
   bd_fric              = 0<br />
   ld_seed              = 1993<br />
   cos_accel            = 0<br />
   deform (3x3):<br />
      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}<br />
      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}<br />
      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}<br />
   userint1             = 0<br />
   userint2             = 0<br />
   userint3             = 0<br />
   userint4             = 0<br />
   userreal1            = 0<br />
   userreal2            = 0<br />
   userreal3            = 0<br />
   userreal4            = 0<br />
grpopts:<br />
   nrdf:         1.5         1.5<br />
   ref_t:           0           0<br />
   tau_t:           0           1<br />
anneal:          No          No<br />
ann_npoints:           0           0<br />
   acc:               0           0           0<br />
   nfreeze:           N           N           N<br />
   energygrp_flags[  0]: 0 0<br />
   energygrp_flags[  1]: 0 0<br />
   efield-x:<br />
      n = 0<br />
   efield-xt:<br />
      n = 0<br />
   efield-y:<br />
      n = 0<br />
   efield-yt:<br />
      n = 0<br />
   efield-z:<br />
      n = 0<br />
   efield-zt:<br />
      n = 0<br />
   bQMMM                = FALSE<br />
   QMconstraints        = 0<br />
   QMMMscheme           = 0<br />
   scalefactor          = 1<br />
qm_opts:<br />
   ngQM                 = 0<br />
Table routines are used for coulomb: TRUE<br />
Table routines are used for vdw:     FALSE<br />
Will do PME sum in reciprocal space.<br />
<br />
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br />
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen<br />
A smooth particle mesh Ewald method<br />
J. Chem. Phys. 103 (1995) pp. 8577-8592<br />
-------- -------- --- Thank You --- -------- --------<br />
<br />
Using a Gaussian width (1/beta) of 0.320163 nm for Ewald<br />
Cut-off's:   NS: 1   Coulomb: 1   LJ: 1<br />
System total charge: 0.000<br />
Generated table with 4000 data points for Ewald.<br />
Tabscale = 2000 points/nm<br />
Generated table with 4000 data points for LJ6.<br />
Tabscale = 2000 points/nm<br />
Generated table with 4000 data points for LJ12.<br />
Tabscale = 2000 points/nm<br />
Configuring nonbonded kernels...<br />
Testing x86_64 SSE2 support... present.<br />
<br />
<br />
Removing pbc first time<br />
Center of mass motion removal mode is Linear<br />
We have the following groups for center of mass motion removal:<br />
  0:  rest<br />
There are: 2 Atoms<br />
Max number of connections per atom is 1<br />
Total number of connections is 2<br />
Max number of graph edges per atom is 1<br />
Total number of graph edges is 2<br />
Initial temperature: 17884.7 K<br />
<br />
Started mdrun on node 0 Tue Jun  2 13:38:03 2009<br />
<br />
           Step           Time         Lambda<br />
              0        0.00000        0.00000<br />
<br />
   Energies (kJ/mol)<br />
        G96Bond        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential<br />
    1.99416e+01    0.00000e+00    0.00000e+00    0.00000e+00    1.99416e+01<br />
    Kinetic En.   Total Energy    Temperature Pressure (bar)<br />
            nan            nan            nan            nan<br />
<br />
           Step           Time         Lambda<br />
              1        0.00010        0.00000<br />
<br />
</p>
<p>
<br />
</p>
<p class="imp-signature">
--<br />
Inon   Sharony<br />
ינון     שרוני<br />
+972(3)6407634<br />
atto.TAU.ac.IL/~inonshar<br />
Please consider your environmental responsibility before printing this e-mail.
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