Hi All,
I am trying to recompute the energies using PMEMD for individual frames from a trajectory generated from a previous PMEMD simulation (under NVT ensemble). However, I get very different VDWAALS and EELEC energies between the recomputed ones and the ones printed in original simulation. Does anyone know how this big difference comes from? It seems different pairlist shouldn't produce such a large different values.
In order to show this problem, I made a simple test using the following scripts (see below). From the comparison, the bonded terms are very close to each other. However, the nonbonded terms (VDWAALS and EELEC) are very different from the original simulation and recomputed simulation.
Is there a way that I can get the same recomputed energies as the ones printed from the original simulation with PMEMD? Any suggestion or explanation is greatly appreciated.
Big thanks!
Mingjun
------------------trajectory generation: 4 frames were recorded from this simulation
test md simulations
&cntrl
! parameters for general MD
imin = 0, nstlim = 200, irest = 0, dt = 0.002,
ntt = 3, temp0 = 298.0, gamma_ln = 2.0, ig = -1,
ntb = 1, mcbarint = 1,
ntp = 0, barostat = 2, pres0 = 1.01325, taup = 2.0,
ntwe = 10, ntwx = 50, ntpr = 1, ntwr = 10, ntave = 10,
ioutfm = 1, iwrap = 1, ntxo = 2,
ntc = 2, ntf = 1,
/
&ewald
/
----------------------The energy components for the 3rd recorded frame:
NSTEP = 151 TIME(PS) = 0.302 TEMP(K) = 230.95 PRESS = 0.0
Etot = -144574.8836 EKtot = 24867.1203 EPtot = -169442.0039
BOND = 907.5497 ANGLE = 2519.4685 DIHED = 4651.2401
1-4 NB = 1345.9908 1-4 EEL = 16351.0887 VDWAALS = 21141.9669
EELEC = -216359.3087 EHBOND = 0.0000 RESTRAINT = 0.0000
Ewald error estimate: 0.3404E-04
=====================PMEMD rerun with the 3rd frame generated from above simulation
rerun md simulations
&cntrl
! parameters for general MD
imin = 0, nstlim = 2, irest = 0, dt = 0.002,
ntt = 3, temp0 = 298.0, gamma_ln = 2.0, ig = -1,
ntb = 1, mcbarint = 1,
ntp = 0, barostat = 2, pres0 = 1.01325, taup = 2.0,
ntwe = 10, ntwx = 50, ntpr = 1, ntwr = 10, ntave = 10,
ioutfm = 1, iwrap = 1, ntxo = 2,
ntc = 2, ntf = 1,
/
&ewald
/
----------------------The energy components for step 0 with the 3rd recorded frame:
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -158202.8866 EKtot = 0.0000 EPtot = -158202.8866
BOND = 907.5465 ANGLE = 2519.4674 DIHED = 4651.2408
1-4 NB = 1345.9908 1-4 EEL = 16351.0884 VDWAALS = 20307.6375
EELEC = -204285.8579 EHBOND = 0.0000 RESTRAINT = 0.0000
Ewald error estimate: 0.4939E-04
----------------------
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Received on Fri May 24 2019 - 03:30:02 PDT
