[gmx-users] Calculate interaction energy dynamically

Davit Hakobyan davhak2000 at hotmail.com
Wed Jul 24 15:25:28 CEST 2013

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
 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
-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

 md rerun 'DPPC/DUPC/CHOLESTEROL BILAYER', reading coordinates from 
input trajectory 

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
               (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:     12.993      1.855 895719.837      0.000


 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.

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
 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) ?

Thanks a lot for all the suggestions.

> Date: Wed, 24 Jul 2013 07:12:54 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Calculate interaction energy dynamically
> On 7/24/13 5:49 AM, Davit Hakobyan wrote:
> This is smelling a bit buggy to me, but then too, I've never tried a rerun on a 
> reordered trajectory.  As a test, can you produce an .edr file from a rerun of 
> the original trajectory (i.e. not manipulated by trjorder)?
> -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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