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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Received on Thu Jan 20 2011 - 13:30:04 PST
