Try visualizing the trajectory with your favorite program (like VMD or
something) and see if you can see any obvious clashes.
Also, did you specify "nobox" in your trajout statement when using ptraj?
Good luck!
Jason
On Wed, Dec 1, 2010 at 3:47 PM, Bongkeun Kim <bkim.chem.ucsb.edu> wrote:
> Hello,
>
> I used igb=5 and igb=6 both, but these gave me too large number and
> NaN error on output.
> --------------------------------
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 1.7889E+21 1.5519E+22 4.7343E+23 CD 307
>
> BOND = 6254035.9830 ANGLE = 72443.8361 DIHED =
> 1478.1915
> VDWAALS = ************* EEL = -6022.1977 EGB =
> 0.0000
> 1-4 VDW = 9715179.9302 1-4 EEL = 836.5689 RESTRAINT =
> 0.0000
> -bash-3.2$ tail 2hb2_equil_x_wat.out
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 NaN NaN 1.1769E+06 CG 145
>
> BOND = ************* ANGLE = 69232.1399 DIHED =
> 1514.8657
> VDWAALS = NaN EEL = +Infinity EGB =
> 0.0000
> 1-4 VDW = -0.0007 1-4 EEL = 104.8996 RESTRAINT =
> 0.0000
> -bash-3.2$ tail 2hb2_equil_x_wat.out
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 1.2140E+08 8.3418E+05 1.1472E+07 OE2 364
>
> BOND = ************* ANGLE = 65089.4218 DIHED =
> 1452.7606
> VDWAALS = 5545981.4707 EEL = -1282.8808 EGB =
> 0.0000
> 1-4 VDW = 533470.1871 1-4 EEL = 891.5496 RESTRAINT =
> 0.0000
> --------------------------------------------------------
>
> I guess it looks like there are some bugs when ptraj extracted coordinates.
>
>
> Quoting Jason Swails <jason.swails.gmail.com>:
>
> > It sounds like it's still trying to use the box information, which it
> really
> > shouldn't if you've stripped the waters. Do you want to run in some kind
> of
> > GB or PB implicit solvent, or just vacuum (gas phase) energies?
> >
> > Try setting the igb variable to the GB model you want to use (or set it
> to 6
> > if you want vacuum). Does this fix your problem?
> >
> > Good luck,
> > Jason
> >
> > On Wed, Dec 1, 2010 at 2:49 PM, Bongkeun Kim <bkim.chem.ucsb.edu> wrote:
> >
> >> Hello,
> >>
> >> I extracted peptide only mdcrd from the explicit water simulation with
> >> the peptide only prmtop file.
> >> And I tried to calculate EPTOT for the peptide with the following input.
> >> =================================
> >> extract energy
> >> &cntrl
> >> imin = 5,
> >> maxcyc = 1,
> >> ntpr=1, ntwx=1,
> >> ntb=0, cut=999
> >> /
> >> =================================
> >>
> >> Error occurs after few steps of calculations like:
> >> ---------------------------------------------
> >> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> >> 1 1.3554E+02 1.8784E+01 8.2938E+01 CG 85
> >>
> >> BOND = 130.6848 ANGLE = 379.7738 DIHED =
> >> 352.5286
> >> VDWAALS = -124.5685 EEL = -2520.8371 HBOND =
> >> 0.0000
> >> 1-4 VDW = 132.3825 1-4 EEL = 1785.5740 RESTRAINT =
> >> 0.0000
> >> minimization completed, ENE= 0.13553800E+03 RMS= 0.187837E+02
> >> minimizing coord set # 2
> >> Frac coord min, max: 0.168166141059582 1.09509660191633
> >> The system has extended beyond
> >> the extent of the virtual box.
> >> Restarting sander will recalculate
> >> a new virtual box with 30 Angstroms
> >> extra on each side, if there is a
> >> restart file for this configuration.
> >> SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
> >> Atom out of bounds. If a restart has been written,
> >> restarting should resolve the error
> >> --------------------------------------------------------
> >>
> >>
> >> I checked mdcrd file and found too large number of coordinates with
> >> less precision.
> >> ---------------------------------------
> >> 1.000 2.000 0.000 3.000 9.000 3.000 4.000 8.000
> >> 9.000 1.000
> >> 1.000 8.000 3.000 5.000 3.000 9.000 5.000 1.000
> >> 0.000 4.000
> >> 5.000 3.000 2.000 9.000 3.000 1.000 3.000 5.000
> >> 2.000 7.000
> >> 6.000 6.000 6.000 2.000 8.000 2.000 8.000 0.000
> >> 7.000 3.000
> >> 0.000 3.000 8.000 8.000 2.000 7.000 4.000 5.000
> >> 6.000 2.000
> >> 0.000 0.000 2.000 4.000 2.000 6.000 5.000 0.000
> >> 3.000 4.000
> >> 9.000 3.000 6.000 4.000 1.000 4.000 5.000 0.000
> >> 1.000 6.000
> >> 2.000 7.000 8.000 5.000 4.000 3.000 6.000 1.000
> >> 1.000 9.000
> >> 6.000 3.000 9.000 6.000 1.000 5.000 1.000 8.000
> >> 0.000 8.000
> >> 7.000 8.000 3.000 5.000 7.000 8.000 6.000 7.000
> >> 8.000 7.000
> >> 7.000 1.000 4.000 7.000 9.000 1.000 0.000 8.000
> >> 9.000 0.000
> >> 7.000 4.000 3.000 2.000 4.000 2.000 8.000 1.000
> >> 7.000 9.000
> >> 5.000 8.000 0.000 0.000 6.000 9.000 1.000 9.000
> >> 1.000 9.000
> >> 7.000 4.000 8.000 2.000 1.000 1.000 2.000 4.000
> >> 4.000 0.000
> >> 0.000 6.000 6.000 8.000 6.000 6.000 9.000 4.000
> >> 1.000 3.000
> >> 8.000 8.000 0.000 6.000 5.000 1.000 1.000 0.000
> >> 8.000 9.000
> >> 1.000 2.000 8.000 7.000 7.000 7.000 1.000 5.000
> >> 0.000 8.000
> >> 5.000 2.000 3.000 7.000 0.000 3.000 2.000 7.000
> >> 3.000 9.000
> >> 7.000 8.000 9.000 0.000 5.000 1.000 7.000 2.000
> >> 9.000 1.000
> >> 9.000 7.000 0.000 2.000 1.000 2.000 1.000 9.000
> >> 41.088 9.420 62.665 41.721 9.148 61.455 41.567 10.044
> >> 35.604 26.216
> >> 21.505 34.680 26.278 21.261 35.621 26.433 22.437 14.278
> >> 11.771 31.180
> >> 13.541 12.366 31.319 14.961 12.321 30.796 16.130 29.593
> >> 25.338 15.722
> >> 30.307 25.829 15.438 29.277 24.757 16.856 41.297 2.102
> >> 17.512 40.872
> >> 2.655 16.070 41.333 2.647 36.490 3.145 5.092 36.652
> >> 4.079 5.219
> >> 37.363 2.759 5.015 7.146 2.097 0.247 7.539 1.234
> >> 0.117 7.889
> >> 2.701 0.249 48.336 17.814 3.189 48.102 16.902 3.019
> >> 49.070 17.762
> >> 3.801 35.401 29.453 25.979 34.841 30.226 25.920 36.101
> >> 29.615 25.346
> >> --------------------------------------------------------------
> >>
> >> I'm using AMBER 11 GPU with the recent bugfix 12.
> >> If you have any idea, please let me know.
> >> Thank you.
> >> Bongkeun Kim
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Dec 01 2010 - 13:00:05 PST
