[gmx-users] Calculate interaction energy dynamically

Davit Hakobyan davhak2000 at hotmail.com
Thu Jul 25 11:13:14 CEST 2013



> Date: Wed, 24 Jul 2013 09:35:26 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Calculate interaction energy dynamically
> 
> 
> 
> On 7/24/13 9:25 AM, Davit Hakobyan wrote:
> > Thank you again for your time and help.
> >
> > Performing "rerun" on the original system passes without warnings with the following output:
> >
> > ----------------------------------------------------------------------------------------------------------------------------
> >
> > Option     Filename  Type         Description
> > ------------------------------------------------------------
> >    -s inp/dyn/dppc_dupc_chol_034x051x015_295K.tpr  Input        Run input
> >                                     file: tpr tpb tpa
> >
> >   -o
> > /scratch/tmp/dhako_01/projects/_rafts_cg/crd/dynmc_restart/dppc_dupc_chol_034x051x015_295K_testrerun.trr
> >   Output       Full precision trajectory: trr trj cpt
> >    -x       traj.xtc  Output, Opt. Compressed trajectory (portable xdr format)
> > -cpi      state.cpt  Input, Opt.  Checkpoint file
> > -cpo      state.cpt  Output, Opt. Checkpoint file
> >    -c crd/dynmc_end/dppc_dupc_chol_034x051x015_295K_testrerun.gro  Output
> >                                     Structure file: gro g96 pdb etc.
> >    -e dat/enr/dppc_dupc_chol_034x051x015_295K_testrerun.edr  Output
> >                                     Energy file
> >    -g out/dppc_dupc_chol_034x051x015_295K_testrerun.log  Output       Log file
> > -dhdl      dhdl.xvg  Output, Opt. xvgr/xmgr file
> > -field    field.xvg  Output, Opt. xvgr/xmgr file
> > -table    table.xvg  Input, Opt.  xvgr/xmgr file
> > -tablep  tablep.xvg  Input, Opt.  xvgr/xmgr file
> > -tableb   table.xvg  Input, Opt.  xvgr/xmgr file
> > -rerun /scratch/tmp/dhako_01/projects/_rafts_cg/crd/dynmc_restart/dppc_dupc_chol_034x051x015_295K.trr
> >   Input, Opt!  Trajectory: xtc trr trj gro g96 pdb cpt
> > -tpi        tpi.xvg  Output, Opt. xvgr/xmgr file
> > -tpid   tpidist.xvg  Output, Opt. xvgr/xmgr file
> >   -ei        sam.edi  Input, Opt.  ED sampling input
> >   -eo        sam.edo  Output, Opt. ED sampling output
> >    -j       wham.gct  Input, Opt.  General coupling stuff
> >   -jo        bam.gct  Output, Opt. General coupling stuff
> > -ffout      gct.xvg  Output, Opt. xvgr/xmgr file
> > -devout   deviatie.xvg  Output, Opt. xvgr/xmgr file
> > -runav  runaver.xvg  Output, Opt. xvgr/xmgr file
> >   -px      pullx.xvg  Output, Opt. xvgr/xmgr file
> >   -pf      pullf.xvg  Output, Opt. xvgr/xmgr file
> > -mtx         nm.mtx  Output, Opt. Hessian matrix
> >   -dn     dipole.ndx  Output, Opt. Index file
> >
> > Option       Type   Value   Description
> > ------------------------------------------------------
> > -[no]h       bool   no      Print help info and quit
> > -[no]version bool   no      Print version info and quit
> > -nice        int    0       Set the nicelevel
> > -deffnm      string         Set the default filename for all file options
> > -xvg         enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
> > -[no]pd      bool   no      Use particle decompostion
> > -dd          vector 0 0 0   Domain decomposition grid, 0 is optimize
> > -nt          int    0       Number of threads to start (0 is guess)
> > -npme        int    -1      Number of separate nodes to be used for PME, -1
> >                              is guess
> > -ddorder     enum   interleave  DD node order: interleave, pp_pme or cartesian
> > -[no]ddcheck bool   yes     Check for all bonded interactions with DD
> > -rdd         real   0       The maximum distance for bonded interactions with
> >                              DD (nm), 0 is determine from initial coordinates
> > -rcon        real   0       Maximum distance for P-LINCS (nm), 0 is estimate
> > -dlb         enum   auto    Dynamic load balancing (with DD): auto, no or yes
> > -dds         real   0.8     Minimum allowed dlb scaling of the DD cell size
> > -gcom        int    -1      Global communication frequency
> > -[no]v       bool   no      Be loud and noisy
> > -[no]compact bool   yes     Write a compact log file
> > -[no]seppot  bool   no      Write separate V and dVdl terms for each
> >                              interaction type and node to the log file(s)
> > -pforce      real   -1      Print all forces larger than this (kJ/mol nm)
> > -[no]reprod  bool   no      Try to avoid optimizations that affect binary
> >                              reproducibility
> > -cpt         real   15      Checkpoint interval (minutes)
> > -[no]cpnum   bool   no      Keep and number checkpoint files
> > -[no]append  bool   yes     Append to previous output files when continuing
> >                              from checkpoint instead of adding the simulation
> >                              part number to all file names
> > -maxh        real   -1      Terminate after 0.99 times this time (hours)
> > -multi       int    0       Do multiple simulations in parallel
> > -replex      int    0       Attempt replica exchange every # steps
> > -reseed      int    -1      Seed for replica exchange, -1 is generate a seed
> > -[no]ionize  bool   no      Do a simulation including the effect of an X-Ray
> >                              bombardment on your system
> >
> > Reading file inp/dyn/dppc_dupc_chol_034x051x015_295K.tpr, VERSION 4.5.1 (single precision)
> > Starting 8 threads
> > Making 2D domain decomposition 4 x 2 x 1
> >
> > WARNING: This run will generate roughly 8779 Mb of data
> >
> > starting
> >   md rerun 'DPPC/DUPC/CHOLESTEROL BILAYER', reading coordinates from
> > input trajectory
> > '/scratch/tmp/dhako_01/projects/_rafts_cg/crd/dynmc_restart/dppc_dupc_chol_034x051x015_295K.trr'
> >
> > trn version: GMX_trn_file (single precision)
> >
> > Reading frame       0 time    0.000
> > Reading frame       1 time 1000.000
> > Reading frame       2 time 2000.000
> > Reading frame       3 time 3000.000
> > Reading frame       4 time 4000.000
> > Reading frame       5 time 5000.000
> > Reading frame       6 time 6000.000
> > Reading frame       7 time 7000.000
> > Reading frame       8 time 8000.000
> > Reading frame       9 time 9000.000
> > Reading frame      10 time 10000.000
> > Reading frame      11 time 11000.000
> > Reading frame      12 time 12000.000
> > Reading frame      13 time 13000.000
> > Reading frame      14 time 14000.000
> > Reading frame      15 time 15000.000
> > Reading frame      16 time 16000.000
> > Reading frame      17 time 17000.000
> > Reading frame      18 time 18000.000
> > Reading frame      19 time 19000.000
> > Reading frame      20 time 20000.000
> > Reading frame      30 time 30000.000
> > Reading frame      40 time 40000.000
> > Reading frame      50 time 50000.000
> > Reading frame      60 time 60000.000
> > Reading frame      70 time 70000.000
> > Reading frame      80 time 80000.000
> > Reading frame      90 time 90000.000
> > Reading frame     100 time 100000.000
> > Reading frame     110 time 110000.000
> > Reading frame     120 time 120000.000
> > Reading frame     130 time 130000.000
> > Reading frame     140 time 140000.000
> > Reading frame     150 time 150000.000
> > Reading frame     160 time 160000.000
> > Reading frame     170 time 170000.000
> > Reading frame     180 time 180000.000
> > Reading frame     190 time 190000.000
> > Reading frame     200 time 200000.000
> > Reading frame     300 time 300000.000
> > Reading frame     400 time 400000.000
> > Reading frame     500 time 500000.000
> > Reading frame     600 time 600000.000
> > Reading frame     700 time 700000.000
> > Reading frame     800 time 800000.000
> > Reading frame     900 time 900000.000
> > Reading frame    1000 time 1000000.000
> > Reading frame    1100 time 1100000.000
> > Reading frame    1200 time 1200000.000
> > Reading frame    1300 time 1300000.000
> > Reading frame    1400 time 1400000.000
> > Reading frame    1500 time 1500000.000
> > Reading frame    1600 time 1600000.000
> > Reading frame    1700 time 1700000.000
> > Reading frame    1800 time 1800000.000
> > Reading frame    1900 time 1900000.000
> > Reading frame    2000 time 2000000.000
> > Reading frame    3000 time 3000000.000
> > Reading frame    4000 time 4000000.000
> > Reading frame    5000 time 5000000.000
> > Reading frame    6000 time 6000000.000
> > Reading frame    7000 time 7000000.000
> > Reading frame    8000 time 8000000.000
> > Reading frame    9000 time 9000000.000
> > Reading frame   10000 time 10000000.000
> > Reading frame   11000 time 11000000.000
> > Reading frame   12000 time 12000000.000
> > Last frame      12000 time 12000000.000
> >
> >   Average load imbalance: 30.8 %
> >   Part of the total run time spent waiting due to load imbalance: 1.7 %
> >
> >
> > NOTE: 6 % of the run time was spent communicating energies,
> >        you might want to use the -gcom option of mdrun
> >
> >
> >      Parallel run - timing based on wallclock.
> >
> >                 NODE (s)   Real (s)      (%)
> >         Time:   1157.505   1157.505    100.0
> >                         19:17
> >                 (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
> > Performance:     12.993      1.855 895719.837      0.000
> >
> > ----------------------------------------------------------------------------------------------------------------------------
> >
> > The
> >   subsequent g_energy also runs smoothly. One gets no warning also if
> > passing the ordered *ordered.tpr and the new index (*ordered.ndx) files
> > to the "mdrun -rerun" of the original system. This indeed leaves with
> > the ordered trajectory file as the only problematic point which might
> > cause the warnings.
> >
> 
> Good to know.
> 
> > Interestingly, the ordered *.trr file
> > (product of trjorder command) is nearly twice as small as the original
> > *.trr file. Since the coordinates in the ordered *.trr file look fine
> > then probably it is the velocities which might be missing in it. Can the
> 
> There's no "might" about it - your gmxcheck output from before shows that 
> velocities are definitely absent, which should account for the difference in 
> file size.
> 
> >   warnings come from this issue ? In this case the g_energy should not be
> >   able to calculate the kinetic energy. If this is the case may one still
> >   rely on the numbers obtained by g_energy for the coulomb and vdw terms
> > (despite the warning messages) ?
> >
> 
> This is a very weird issue.  The .trr file clearly has step and time information 
> (from your earlier post), but the resulting .edr file from mdrun -rerun does not 
> have the correct step number (though it appears to have time).  Your problem 
> does not derive from anything to do with velocities, as far as I can tell. 
> Proceed carefully and scrutinize the output to see if it indeed makes sense - 
> you can verify energy values from snapshots that have not been ordered by 
> creating index files that correspond to the same lipids, for instance.  This is 
> a very non-standard exercise, so it's probably never been tested and debugged.

The energy calculation between the nearest neighbors at a given time frame based on the original trajectory file (with help of new index file) indeed gives the same values as for the ordered trajectory file. So one can probably rely on the energy output from the ordered trajectory despite the warnings.

In case of more information about the warnings I will write in this thread.

Thank you very much for all the help.

> 
> -Justin
> 
> -- 
> ==================================================
> 
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> 
> ==================================================
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