[gmx-users] log file not writing simulation time in continuous manner

[anu chandra]

Dear Gromcas users,


I have used grompp, as shown below, to generate .tpr file in order to
continue the simulation.

gmx_mpi grompp -f md.mdp -o MD5.tpr -c MD4.gro -t MD4.cpt -r ref.pdb -n
index.ndx -p topol.top


My mdp input parameters are shown below,

***************************************************************
define                  = -DPOSRES
integrator              = md
dt                      = 0.002
nsteps                  = 2500000
nstlog                  = 1000
nstxout                 = 5000
nstvout                 = 5000
nstfout                 = 5000
nstcalcenergy           = 100
nstenergy               = 1000
;
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
;
tcoupl                  = Nose-Hoover
tc_grps                 = PROT   NPROT   SOL_ION
tau_t                   = 1.0    1.0     1.0
ref_t                   = 303.15 303.15 303.15
;
pcoupl                  = Parrinello-Rahman
pcoupltype              = semiisotropic
tau_p                   = 5.0     5.0
compressibility         = 4.5e-5  4.5e-5
ref_p                   = 1.0     1.0
;
constraints             = h-bonds
constraint_algorithm    = LINCS
continuation            = yes
;
gen-vel                 = no
;
nstcomm                 = 100
comm_mode               = linear
comm_grps               = PROT   NPROT   SOL_ION
;
refcoord_scaling        = com

*******************************************************************

Unfortunately log file shows simulation time as a new start, not as
continuation from previous run, as shown below. Time suppose to start from
10001 ps.

******************************************************************************************
Started mdrun on rank 0 Sat Aug 15 13:15:04 2015
           Step          *Time*         Lambda
              0        *0.00000 *       0.00000

   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    2.70981e+04    1.28824e+05    9.76982e+04    2.20959e+03    2.96128e+02
          LJ-14     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.
    1.93530e+04   -3.84842e+04    7.57381e+04   -1.87856e+06    7.47371e+03
 Position Rest.     Dih. Rest.      Potential    Kinetic En.   Total Energy
    1.93759e+03    0.00000e+00   -1.55642e+06    4.40783e+05   -1.11564e+06
    Temperature Pressure (bar)   Constr. rmsd
    3.03457e+02    2.41812e+02    3.91153e-06

DD  step 24 load imb.: force 21.2%  pme mesh/force 0.689

At step 25 the performance loss due to force load imbalance is 9.0 %

NOTE: Turning on dynamic load balancing

DD  step 999  vol min/aver 0.816  load imb.: force  1.5%  pme mesh/force
0.768

           Step           *Time*         Lambda
           1000        *2.00000*        0.00000

   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    2.70890e+04    1.29741e+05    9.79287e+04    2.28826e+03    2.58526e+02
          LJ-14     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.
    1.94561e+04   -3.80345e+04    7.15659e+04   -1.87484e+06    7.69793e+03
 Position Rest.     Dih. Rest.      Potential    Kinetic En.   Total Energy
    2.00424e+03    0.00000e+00   -1.55485e+06    4.41080e+05   -1.11377e+06
    Temperature Pressure (bar)   Constr. rmsd
    3.03661e+02    1.71385e+02    3.91311e-06
*************************************************************************************************

Can any body help me to figure this out?

Many thanks in advance

Anu