Hello,
I have been running MD simulations using Amber 10 and 11 before, however, I
recently switched to Amber 12 due to its efficient computational capacity.
The same systems I have previously ran in Amber are now unexpectedly
blowing up after several nanoseconds of production while using GPU (CUDA)
Version of PMEMD version 12.1. Additionally, the system continues to run
even with the "******" up until the maximum steps I put in the input file
although the energy values and densities do not make sense. Using VMD,
nothing visually appears to be out of the ordinary and this did not happen
using prior versions of Amber. The whole last "bad" restart file contains
all ****** and thus cannot be used for future simulations. It was suggested
to me to use iwrap=1, but this still occurs even with iwrap=1.
Additionally, using the check overlap tool on the trajectory files, no
atoms were listed to be within the default values so I'm not sure why this
is still happening. If I restart the simulation from my last good restart
file, everything runs fine for several more nanoseconds. Energies and
densities look stable before the "blow up".
Although the simulation goes back to normal if I use the last good restart
file of my simulation, I just want to make sure there is not something very
wrong with my system. Below is my input file as well as a section of the
output file that contains the "*******" and as mentioned, the simulation
keeps going until the max number of steps but clearly the energy values and
density values do not make sense.
Input :
&cntrl
imin = 0, irest=1, ntx=5,
ntb=2, ntp=1, taup=1.0,
pres0=0.98,
ig=-1,
iwrap=1,
cut = 15.0,
ntc=2, ntf=2,
temp0=298.0,
ntt=3, gamma_ln=5,
nstlim= 1000000, dt =0.002,
ntpr=1000, ntwx= 1000, ntwr = 1000
&end
Section of Output:
NSTEP = 87000 TIME(PS) = 15802.000 TEMP(K) = 331.33 PRESS =
-277.3
Etot = -137358.4935 EKtot = 9086.1172 EPtot =
-146444.6107
BOND = 3244.8075 ANGLE = 5467.3853 DIHED =
7265.7719
1-4 NB = 188.2156 1-4 EEL = -187788.4759 VDWAALS =
-5104.3570
EELEC = 30282.0419 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 1222.6766 VIRIAL = 1870.1499 VOLUME =
108126.1735
Density =
1.1967
------------------------------------------------------------------------------
wrapping first mol.: 758055.52943 122927.92369-12401192.44732
wrapping first mol.: 758055.52943 122927.92369-12401192.44732
NSTEP = 88000 TIME(PS) = 15804.000 TEMP(K) =********* PRESS =
6204.7
Etot = ************** EKtot = ************** EPtot =
**************
BOND = 0.0000 ANGLE = 1198214.2838 DIHED =
23509.4222
1-4 NB = 0.0000 1-4 EEL = -4.2558 VDWAALS =
**************
EELEC = 42304898.1122 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 12582912.0000 VIRIAL = 5661878.4412 VOLUME =
51661802.8483
Density =
0.0025
------------------------------------------------------------------------------
wrapping first mol.: 987146.16498 289271.90065-31488848.29287
wrapping first mol.: 987146.16498 289271.90065-31488848.29287
NSTEP = 89000 TIME(PS) = 15806.000 TEMP(K) =********* PRESS =
6174.0
Etot = ************** EKtot = ************** EPtot =
89020168.5599
BOND = 0.0000 ANGLE = 1347576.8634 DIHED =
23526.4752
1-4 NB = 0.0000 1-4 EEL = -5.6433 VDWAALS =
11598652.0389
EELEC = 76050418.8256 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 12582912.0000 VIRIAL = -754075.8966 VOLUME =
100049641.6333
Density =
0.0013
------------------------------------------------------------------------------
Please let me know if you need any additional information or have an idea
as to what could be happening, I realize this could be system specific if
it's something with my parameters, however, I figured it would have
appeared earlier in the simulation if that was the case. I'm using GAFF
default values with charges I obtained through Gaussian.
Thanks for your time and help,
Sasha Perkins
Penn State MatSE graduate student
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Received on Fri Nov 09 2012 - 19:30:02 PST
