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

[anu chandra]

Dear Justin,

Thanks a lot for your prompt reply.

On Sat, Aug 15, 2015 at 2:55 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
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