[gmx-users] some problems by freshman

zpxu zp.xu at mf.mpg.de
Thu Aug 15 21:17:36 CEST 2002


It's my md.log:
Thanks very much.
-------------------------------
There are 0 atoms for free energy perturbation
Input Parameters:
   integrator           = steep
   nsteps               = 100
   ns_type              = Grid
   nstlist              = 10
   ndelta               = 2
   bDomDecomp           = FALSE
   decomp_dir           = 0
   nstcomm              = 1
   nstlog               = 100
   nstxout              = 100
   nstvout              = 100
   nstfout              = 0
   nstenergy            = 100
   nstxtcout            = 0
   init_t               = 0
   delta_t              = 0.002
   xtcprec              = 1000
   nkx                  = 0
   nky                  = 0
   nkz                  = 0
   pme_order            = 4
   ewald_rtol           = 1e-05
   ewald_geometry       = 0
   epsilon_surface      = 0
   optimize_fft         = FALSE
   ePBC                 = xyz
   bUncStart            = FALSE
   bShakeSOR            = FALSE
   etc                  = No
   epc                  = No
   epctype              = Isotropic
   tau_p                = 1
   ref_p (3x3):
      ref_p[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      ref_p[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      ref_p[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   compress (3x3):
      compress[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      compress[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      compress[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   bSimAnn              = FALSE
   zero_temp_time       = 0
   rlist                = 1
   coulombtype          = Cut-off
   rcoulomb_switch      = 0
   rcoulomb             = 1
   vdwtype              = Cut-off
   rvdw_switch          = 0
   rvdw                 = 1
   epsilon_r            = 1
   DispCorr             = No
   fudgeQQ              = 1
   free_energy          = no
   init_lambda          = 0
   sc_alpha             = 0
   sc_sigma             = 0.3
   delta_lambda         = 0
   disre_weighting      = Conservative
   disre_mixed          = FALSE
   dr_fc                = 1000
   dr_tau               = 0
   nstdisreout          = 100
   orires_fc            = 0
   orires_tau           = 0
   nstorireout          = 100
   em_stepsize          = 0.01
   em_tol               = 100
   niter                = 20
   fc_stepsize          = 0
   nstcgsteep           = 1000
   ConstAlg             = Lincs
   shake_tol            = 0.0001
   lincs_order          = 4
   lincs_warnangle      = 30
   bd_temp              = 300
   bd_fric              = 0
   ld_seed              = 1993
   cos_accel            = 0
   userint1             = 0
   userint2             = 0
   userint3             = 0
   userint4             = 0
   userreal1            = 0
   userreal2            = 0
   userreal3            = 0
   userreal4            = 0
grpopts:
   nrdf:         1197
   ref_t:            0
   tau_t:            0
   acc:            0           0           0
   nfreeze:           N           N           N
   energygrp_excl[  0]: 0
   efield-x:
      n = 0
   efield-xt:
      n = 0
   efield-y:
      n = 0
   efield-yt:
      n = 0
   efield-z:
      n = 0
   efield-zt:
      n = 0
CPU=  0, lastcg=  399, targetcg=  200, myshift=    0
nsb->shift =   1, nsb->bshift=  0
Neighbor Search Blocks
nsb->nodeid:         0
nsb->nnodes:      1
nsb->cgtotal:   400
nsb->natoms:    400
nsb->shift:       1
nsb->bshift:      0
Nodeid   index  homenr  cgload  workload
     0       0     400     400       400

Max number of bonds per atom is 3
Table routines are used for coulomb: FALSE
Table routines are used for vdw:     FALSE
Cut-off's:   NS: 1   Coulomb: 1   LJ: 1
Generated table with 500 data points for COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 1 molecules, 400 charge groups and 400 atoms
There are 0 optimized solvent molecules on node 0
There are 0 optimized water molecules on node 0
Initiating Steepest Descents
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest, initial mass: 4804.41
Started Steepest Descents on node 0 Thu Aug 15 21:11:46 2002
Removing pbc first time
Done rmpbc
Steepest Descents:
   Tolerance         =  1.00000e+02
   Number of steps   =          100
Grid: 40 x 40 x 100 cells
           Step           Time         Lambda      Annealing
              0        0.00000        0.00000        0.00000

           Step           Time         Lambda      Annealing
              1        1.00000        0.00000        0.00000

   Energies (kJ/mol)
          Morse       G96Angle        LJ (SR)   Coulomb (SR)      Potential
    3.37389e+02    5.48309e+05    2.54048e+08    0.00000e+00    2.54597e+08
    Kinetic En.   Total Energy    Temperature Pressure (bar)
    0.00000e+00    0.00000e+00    0.00000e+00    0.00000e+00

           Step           Time         Lambda      Annealing
              2        2.00000        0.00000        0.00000
......

           Step           Time         Lambda      Annealing
            100      100.00000        0.00000        0.00000

   Energies (kJ/mol)
          Morse       G96Angle        LJ (SR)   Coulomb (SR)      Potential
    7.36535e+04    4.56517e+05    4.03326e+04    0.00000e+00    5.70503e+05
    Kinetic En.   Total Energy    Temperature Pressure (bar)
    0.00000e+00    0.00000e+00    0.00000e+00    0.00000e+00


Steepest Descents did not converge in 100 steps
  Potential Energy  =  5.70503e+05
Maximum force:  4.03849e+04

 M E G A - F L O P S   A C C O U N T I N G

   RF=Reaction-field  Free=Free Energy  SC=Softcore
   T=Tabulated        S=Solvent         W=Water     WW=Water-Water

           Computing:      M-Number      M-Flop's  % Flop's
                   LJ      2.569059     79.640829    39.3
      Innerloop-Iatom      0.040331      0.403310     0.2
             NS-Pairs      4.776331    100.302951    49.5
         Reset In Box      0.040400      0.363600     0.2
              Shift-X      0.040400      0.242400     0.1
               CG-CoM      0.040400      1.171600     0.6
               Angles      0.106050     17.286150     8.5
        Morse Potent.      0.056055      3.251190     1.6
               Virial      0.002727      0.049086     0.0
          Total                   202.71112   100.0

               NODE (s)   Real (s)      (%)
       Time:      2.000      2.000    100.0
Finished mdrun on node 0 Thu Aug 15 21:11:48 2002
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