Dear Amber Users,
I was running a simulation which got stalled after a
period due to some reason. I was saving the restart file (.rst) every
one nanosecond. Hence I restarted the job with the latest restart file
as input. Then I compared the energy values in the beginning of the
new run and the value at the same time step in the old simulation.
I was expecting the energy values to be identical. However they are
not. Below are the values from the two simulation run.
NEW SIMULATION:
NSTEP = 500 TIME(PS) = 32531.000 TEMP(K) = 301.10 PRESS = 39.9
Etot = -94460.3737 EKtot = 23209.8266 EPtot =
-117670.2004
BOND = 596.0055 ANGLE = 1584.8678 DIHED =
1982.9901
1-4 NB = 675.1219 1-4 EEL = 7437.2640 VDWAALS =
14792.4105
EELEC = -144738.8602 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 10380.1481 VIRIAL = 10052.1785 VOLUME =
380816.0028
Density =
1.0110
Ewald error estimate: 0.1281E-03
------------------------------------------------------------------------------
OLD SIMULATION:
NSTEP = 16000500 TIME(PS) = 32531.000 TEMP(K) = 302.19 PRESS = -128.7
Etot = -94254.9707 EKtot = 23294.4062 EPtot =
-117549.3769
BOND = 602.1720 ANGLE = 1558.0063 DIHED =
1989.9839
1-4 NB = 688.5245 1-4 EEL = 7435.4022 VDWAALS =
14663.2548
EELEC = -144486.7205 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 10496.6578 VIRIAL = 11554.9064 VOLUME =
380809.5500
Density =
1.0110
Ewald error estimate: 0.7322E-05
------------------------------------------------------------------------------
I would expect the values to be identical in both cases since I am
restarting my simulation with the same coordinate and velocity values
at this particular time step supplied through restart file.
Am I not correct or am I missing some important fundamental concept?
I will be glad if you can give me your opinion.
Thank you,
Dilraj.
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Received on Sat Feb 25 2012 - 01:00:02 PST
