Hello Amber Users,
The following output occurred in the middle of the calculation and
eventually the whole simulation completed successfully. However, the
trajectory file is smaller than half the size as it's supposed to be and
the restart file is not able to be read (full of "NaN"s) for the next
simulation. It was run on a GTX 680.
Here's the input used for this simulation:
&cntrl
imin=0, irest=0, ntx=1,
ntpr=1000, ntwx=1000, nstlim=2500000,
dt=0.002, ntt=1, tempi=300,
temp0=300, tautp=10.0, ig=-1,
ntp=1, ntc=2, ntf=2, cut=8,
ntb=2, iwrap=1, ioutfm=1,
/
And the output where the abnormal occurred:
------------------------------------------------------------------------------
check COM velocity, temp: 0.000023 0.00(Removed)
NSTEP = 1026000 TIME(PS) = 52422.000 TEMP(K) = 301.97 PRESS =
71.4
Etot = -264506.5286 EKtot = 54510.7109 EPtot =
-319017.2395
BOND = 1934.2114 ANGLE = 5117.7595 DIHED =
10601.7837
1-4 NB = 2209.5364 1-4 EEL = 23527.0220 VDWAALS =
47715.1855
EELEC = -410122.7381 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 23920.8061 VIRIAL = 22577.1270 VOLUME =
871623.4215
Density =
1.0398
------------------------------------------------------------------------------
check COM velocity, temp: NaN NaN(Removed)
wrapping first mol.: NaN NaN NaN
wrapping first mol.: NaN NaN NaN
NSTEP = 1027000 TIME(PS) = 52424.000 TEMP(K) = NaN PRESS
=148483.3
Etot = NaN EKtot = NaN EPtot =
**************
BOND = ************** ANGLE = 1219612.6396 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
-658.3916
EELEC = ************** EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 12582912.0000 VIRIAL = -635655.0059 VOLUME =
4123147.9663
Density =
0.2198
------------------------------------------------------------------------------
wrapping first mol.: NaN NaN NaN
check COM velocity, temp: NaN NaN(Removed)
wrapping first mol.: NaN NaN NaN
wrapping first mol.: NaN NaN NaN
NSTEP = 1028000 TIME(PS) = 52426.000 TEMP(K) = NaN PRESS =
10330.2
Etot = NaN EKtot = NaN EPtot =
**************
BOND = ************** ANGLE = 1219612.6396 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
**************
EELEC = ************** EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 12582912.0000 VIRIAL = 11404.4736 VOLUME =
56364035.4187
Density =
0.0161
------------------------------------------------------------------------------
wrapping first mol.: NaN NaN NaN
check COM velocity, temp: NaN NaN(Removed)
wrapping first mol.: NaN NaN NaN
wrapping first mol.: NaN NaN NaN
NSTEP = 1029000 TIME(PS) = 52428.000 TEMP(K) = NaN PRESS =
3158.1
Etot = NaN EKtot = NaN EPtot =
**************
BOND = ************** ANGLE = 1219612.6396 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
-25.3303
EELEC = ************** EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 12582912.0000 VIRIAL = 5274644.2904 VOLUME =
107179117.4472
Density =
0.0085
------------------------------------------------------------------------------
Did anyone come across this issue and how can I fix it? Any help would be
greatly appreciated.
Best,
Richard
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Received on Thu Aug 08 2013 - 12:00:02 PDT
