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

[Justin Lemkul]

On 8/15/15 9:51 AM, anu chandra wrote:
> 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?
>

If you continue via grompp, you need to set tinit and init_step to get 
continuous output.  Continuing via the convert-tpr/mdrun -cpi approach will 
continue seamlessly.  If you have provided all of the correct inputs to grompp, 
the physics is fine; you just need to post-process when concatenating the 
trajectories (trjcat -settime).

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================