[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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