[gmx-users] Extending Simulation

[bharat gupta]

Dear Gmx Users,

I extended a previously ran 10ns simulation by another 15ns by using the
following commands :-
tpbconv -s mdrun.tpr -extend 15000 -o next.tpr
mpirun -np 24 mdrun -s next.tpr -cpi mdrun.cpt -append -v

The number of frames for 10ns simulation were (5001) and when I checked the
extended simulation for the number of frames using gmxcheck, I still shows
the same number of frames. I want to know  does the new frames got appended
into old mdrun.trr file as I didn't find any new files, after the
simulation got complete...?? Please reply as I am worried whether I made a
mistake during the run or I have to repeat everything again ??

The new md.log that was created during extension run says that It has
finished the job .... Here's the output  of that file :-

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

    Statistics over 7500001 steps using 1500001 frames

   Energies (kJ/mol)
          Angle    Proper Dih. Ryckaert-Bell.          LJ-14     Coulomb-14
    7.43320e+03    4.33773e+02    3.13712e+03    5.20755e+03    2.55855e+04
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
    1.37057e+05   -3.56695e+03   -8.60656e+05   -1.20018e+05   -8.05388e+05
    Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure (bar)
    1.29739e+05   -6.75649e+05    3.00003e+02   -2.30179e+02    1.02839e+00
   Constr. rmsd
    0.00000e+00

          Box-X          Box-Y          Box-Z
    8.01379e+00    8.01379e+00    8.01379e+00

   Total Virial (kJ/mol)
    4.32011e+04   -1.12514e+01    1.49578e+01
   -1.14462e+01    4.32407e+04   -1.98925e+01
    1.50236e+01   -1.97905e+01    4.32529e+04

   Pressure (bar)
    7.72036e-01    4.99560e-02    7.81549e-02
    6.25159e-02    1.42349e+00    5.98871e-02
    7.39076e-02    5.32977e-02    8.89654e-01

   Total Dipole (D)
   -5.60499e+02   -2.55882e+01    2.86784e+02

      T-Protein  T-non-Protein
    2.99927e+02    3.00008e+02


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

   RF=Reaction-Field  FE=Free Energy  SCFE=Soft-Core/Free Energy
   T=Tabulated        W3=SPC/TIP3p    W4=TIP4p (single or pairs)
   NF=No Forces

 Computing:                               M-Number         M-Flops  % Flops
-----------------------------------------------------------------------------
 Coul(T)                            2322605.564626    97549433.714     2.2
 Coul(T) [W3]                         90832.189311    11354023.664     0.3
 Coul(T) + LJ                       3659809.502236   201289522.623     4.6
 Coul(T) + LJ [W3]                   619230.648641    85453829.512     2.0
 Coul(T) + LJ [W3-W3]               8207387.474804  3135222015.375    71.8
 Outer nonbonded loop               1710895.494912    17108954.949     0.4
 1,4 nonbonded interactions           71302.509507     6417225.856     0.1
 Calc Weights                       1170742.656099    42146735.620     1.0
 Spread Q Bspline                  24975843.330112    49951686.660     1.1
 Gather F Bspline                  24975843.330112   149855059.981     3.4
 3D-FFT                            40778435.437124   326227483.497     7.5
 Solve PME                           612360.081648    39191045.225     0.9
 NS-Pairs                           5720973.688414   120140447.457     2.7
 Reset In Box                         26080.500000       78241.500     0.0
 CG-CoM                               78049.552033      234148.656     0.0
 Angles                               49455.006594     8308441.108     0.2
 Propers                               5557.500741     1272667.670     0.0
 RB-Dihedrals                         55447.507393    13695534.326     0.3
 Virial                               79264.552843     1426761.951     0.0
 Stop-CM                              39024.854066      390248.541     0.0
 Calc-Ekin                           390247.604066    10536685.310     0.2
 Lincs                                46919.336729     2815160.204     0.1
 Lincs-Mat                          1003759.241988     4015036.968     0.1
 Constraint-V                        456988.721878     3655909.775     0.1
 Constraint-Vir                       82013.920657     1968334.096     0.0
 Settle                              121050.016140    39099155.213     0.9
-----------------------------------------------------------------------------
 Total                                              4369403789.450   100.0
-----------------------------------------------------------------------------

....
Parallel run - timing based on wallclock.

               NODE (s)   Real (s)      (%)
       Time: 307946.589 307946.589    100.0
                       3d13h32:26
               (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:    266.212     14.189      4.209      5.703
Finished mdrun on node 0 Fri Nov 22 23:33:13 2013

Regards
-----------
Bharat