[gmx-users] A query about nsteps

anu chandra anu80125 at gmail.com
Thu Aug 20 13:49:54 CEST 2015


Dear gromcas users,

I carried out a continuation of previous md run for nsteps of 5000000 and
dt of  0.002 using the following commands,

gmx grompp -f md.mdp -o md2.tpr -c md1.gro -t md1.cpt -r ref.pdb -n
index.ndx -p topol.top

gmx_mpi mdrun -cpi md1.cpt -deffnm md2


The mdp file following run parameters,

***************************************************
integrator              = md
dt                      = 0.002
nsteps                  = 5000000
;
nstlog                  = 1000
nstxout                 = 0
nstvout                 = 0
nstfout                 = 0
nstcalcenergy           = 100
nstenergy               = 1000
nstxout-compressed      = 20000
compressed-x-grps       = System
;
cutoff-scheme           = Verlet
nstlist                 = 20
rlist                   = 1.2
coulombtype             = pme
rcoulomb                = 1.2
vdwtype                 = Cut-off
vdw-modifier            = Force-switch
rvdw_switch             = 1.0
rvdw                    = 1.2
;
pbc                     = xyz
;
gen_vel                 = no
;
tcoupl                  = Nose-Hoover
tc_grps                 = Protein POPC CL_SOL
tau_t                   = 0.5    0.5     0.5
ref_t                   = 305.0    305.0    305.0
;
pcoupl                  = Parrinello-Rahman
pcoupltype              = semiisotropic
tau_p                   = 5.0
compressibility         = 4.5e-5   4.5e-5
ref_p                   = 1.0     1.0
;
constraints             = h-bonds
constraint_algorithm    = LINCS
continuation            = yes
;
nstcomm                 = 100
comm_mode               = linear
comm_grps               = Protein_POPC CL_SOL
;
refcoord_scaling        = com
**************************************************************

Though the run completed successfully, I just noticed from the log file
that the simulation carried out only for 3500000 steps, instead of 5000000
steps. It looks to me that the simulation started from the previous run
that completed 1500000 steps and the current run went from the next 3500000
steps to complete the total run for 5000000 steps. Why this happened? Why
it counted total run as 5000000 steps rather than continue the current for
another 5000000 steps?

Also, I also noticed that the XTC file is written with 176 frames instead
of 175 frames (i.e. 3500000/20000)? Is it writing the last step of the
previous run again?

Below is the head and tail of the log file.

***************************************************
Started mdrun on rank 0 Wed Aug 19 13:21:50 2015
           Step           Time         Lambda
        1500000     3000.00000        0.00000

   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    2.68385e+04    1.29842e+05    9.81752e+04    2.12606e+03    1.22039e+02
          LJ-14     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.
    1.92413e+04   -3.79314e+04    8.94538e+04   -2.15678e+06    8.56903e+03
 Position Rest.      Potential    Kinetic En.   Total Energy
    1.19967e+03      -1.81913e+06    4.40840e+05   -1.37829e+06
    Temperature Pressure (bar)   Constr. rmsd
    3.05915e+02    9.88325e+01    3.99434e-06

DD  step 1500024 load imb.: force 23.7%  pme mesh/force 0.689

At step 1500025 the performance loss due to force load imbalance is 10.2 %

NOTE: Turning on dynamic load balancing

DD  load balancing is limited by minimum cell size in dimension Z
DD  step 1500999  vol min/aver 0.797! load imb.: force  2.1%  pme
mesh/force 1.021

           Step           Time         Lambda
        1501000     3002.00000        0.00000

   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    2.69950e+04    1.30117e+05    9.81626e+04    2.14421e+03    3.04253e+02
          LJ-14     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.
    1.92568e+04   -3.91777e+04    8.75313e+04   -2.15233e+06    8.72461e+03
 Position Rest.      Potential    Kinetic En.   Total Energy
    1.12669e+03     -1.81713e+06    4.39962e+05   -1.37717e+06
    Temperature Pressure (bar)   Constr. rmsd
    3.05306e+02   -1.47275e+02    3.98818e-06
---------------------------------------------
---------------------------------------------
---------------------------------------------
           Step           Time         Lambda
        5000000    10000.00000        0.00000

Writing checkpoint, step 5000000 at Wed Aug 19 22:49:38 2015


   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    2.71898e+04    1.29717e+05    9.78396e+04    2.14084e+03    1.91548e+02
          LJ-14     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.
    1.92444e+04   -3.67507e+04    9.10908e+04   -2.16220e+06    8.48970e+03
 Position Rest.      Potential    Kinetic En.   Total Energy
    1.26666e+03     -1.82178e+06    4.38586e+05   -1.38319e+06
    Temperature Pressure (bar)   Constr. rmsd
    3.04350e+02    7.56441e+01    3.99781e-06

        <======  ###############  ==>
        <====  A V E R A G E S  ====>
        <==  ###############  ======>

        Statistics over 3500001 steps using 35001 frames

   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    2.71537e+04    1.29908e+05    9.80926e+04    2.22652e+03    1.80928e+02
          LJ-14     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.
    1.91048e+04   -3.81235e+04    8.95751e+04   -2.15651e+06    8.65871e+03
 Position Rest.      Potential    Kinetic En.   Total Energy
    1.19417e+03     -1.81854e+06    4.39526e+05   -1.37901e+06
    Temperature Pressure (bar)   Constr. rmsd
    3.05003e+02    1.27530e+00    0.00000e+00
*********************************************************************************

Many thanks

Anu


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