Hello,
While Ross knows this code probably much better than I do, I think he missed
something small (but seriously important in this case) regarding your email.
The amber11's bugfixes no longer have coincidentally matching bugfixes.
That is to say, the Amber11 bug fixes now go up to 12 (you say you applied
up to 11).
The 12th bugfix addresses these issues when you use a cutoff value > 8
(which you are; yours is 10).
Apply bugfix 12 and all should be well.
Good luck!
Jason
On Thu, Jan 20, 2011 at 4:14 PM, Bongkeun Kim <bkim.chem.ucsb.edu> wrote:
> Hello,
>
> I got NaN error when I ran pmemd.cuda and pmemd.cuda.mpi about after 50ns.
> The log file is like:
>
> NSTEP = 1465000 TIME(PS) = 52980.000 TEMP(K) = 358.79 PRESS
> = 71.4
> Etot = -62655.3195 EKtot = 27682.3184 EPtot =
> -90337.6379
> BOND = 2126.8615 ANGLE = 1531.3712 DIHED =
> 1681.7735
> 1-4 NB = 8574.2946 1-4 EEL = 1833.2170 VDWAALS =
> 8865.3186
> EELEC = -114950.4742 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 12293.6612 VIRIAL = 11676.7751 VOLUME =
> 399930.2222
> Density =
> 0.9998
>
>
> ------------------------------------------------------------------------------
>
> wrapping first mol.: -31.3208124120934 0.00000000000000
> 0.00000000000000
> wrapping first mol.: -31.3208124120934 0.00000000000000
> 0.00000000000000
>
> NSTEP = 1470000 TIME(PS) = 52990.000 TEMP(K) = 362.41 PRESS
> = 48.4
> Etot = -62667.6518 EKtot = 27961.6172 EPtot =
> -90629.2690
> BOND = 2136.8358 ANGLE = 1550.7648 DIHED =
> 1682.5454
> 1-4 NB = 8527.4693 1-4 EEL = 1853.5058 VDWAALS =
> 8696.1619
> EELEC = -115076.5520 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 12447.5954 VIRIAL = 12029.4233 VOLUME =
> 400265.4168
> Density =
> 0.9990
>
>
> ------------------------------------------------------------------------------
>
> wrapping first mol.: NaN NaN
> NaN
> wrapping first mol.: NaN NaN
> NaN
>
> NSTEP = 1475000 TIME(PS) = 53000.000 TEMP(K) = NaN PRESS
> = NaN
> Etot = NaN EKtot = NaN EPtot =
> NaN
> BOND = ************** ANGLE = 585786.5880 DIHED =
> 0.0000
> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
> -662.1176
> EELEC = NaN EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 0.0000 VIRIAL = NaN VOLUME =
> NaN
> Density =
> NaN
>
>
> ------------------------------------------------------------------------------
>
>
>
> It was really strange. I set up T=325K and this was well maintained in
> the beginning but at certain point this temperature was growing up and
> finally I got NaN error. When I checked the last rst file before NaN
> error, there is no coordinates and velocities for water molecules and
> the box size is bigger than the one in the beginning.
> +++++++++++++++++++++++++++++++++++++++
> 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
> 31.3730000 80.7640000 158.3730000 90.0000000 90.0000000 90.0000000
> +++++++++++++++++++++++++++++++++++++++++
>
> This is the last part of the rst file from the previous run.
> ++++++++++++++++++++++++++++
> 0.2813319 0.2859586 0.1069026 -0.2630481 0.7645880 0.1471529
> -0.8100536 1.2586927 0.1523881 0.2990605 0.1620192 0.0976196
> -0.0732898 1.1917989 -1.0429825 0.2014995 0.3834629 -0.1202106
> 0.0276703 -0.2488241 -0.2628807 -0.2085400 0.4762971 0.4179272
> -0.3814862 -0.2374063 -0.2416039 0.0699310 -0.0610051 -0.1580978
> 0.9372542 1.0430179 -0.7452719 0.3271696 -0.9559725 -0.3386399
> 0.2260832 0.0151047 0.1283436 1.2348834 -1.0930565 0.2119684
> -0.7740772 0.0938291 0.2359591 0.2605087 0.0407511 -0.3941893
> 2.2260764 -0.6258161 0.5861404 -0.4234042 0.2330984 -0.6828126
> 85.0975010 80.6688215 55.6648514 90.0000000 90.0000000 90.0000000
> +++++++++++++++++++++++++++++++
>
> My input file is this:
> ++++++++++++++++++++++++
> &cntrl
> imin = 0, irest = 1, ntx = 5,
> ntb = 2, pres0 = 1.0, ntp = 2,
> taup = 2.0, iwrap=1,
> cut = 10.0, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 325.0, temp0 = 325.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 5000000, dt = 0.002,
> ntpr = 5000, ntwx = 5000, ntwr = 5000
> /
> +++++++++++++++++++++++++
>
> And I use amber 11 with bugfix 11.
> Please let me know any idea that helps me to avoid this problem.
> Thank you.
> Bongkeun Kim
> bkim.chem.ucsb.edu
>
>
>
>
> _______________________________________________
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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 Thu Jan 20 2011 - 18:00:02 PST
