# AMBER: Question about NVE simulation.

From: <tanc.uci.edu>
Date: Mon, 17 Oct 2005 22:45:51 -0700 (PDT)

Dear All,

I have a question about the NVE simulation. The system I studied
was the 1PGB molecule in gas phase. After minimization and 40ps
NVT, I turned on the NVE (Shake turn on, dt = 0.001), but with
irest = 0. I printed out the results of every step, and my
question is, why the Etot of the first three steps (NSTEP = 0, 1,
2) were so different with the rest? It looks like the Etot keeps
constant only after NSTEP = 3, so what are the real meanings of
the first three Etot? I also tried without Shake, this time the
first three Etot did not show obvious difference (and the results
of NSTEP =0 and 1 are exactly the same,why?), but the fluctuation
of each step looked larger than Shake on.

Best,
Chuck

Following are the mdin file and part of the mdout files:
mdin with SHAKE
&cntrl
imin = 0,
irest = 0, ntx = 1,
ntb = 0,
ntt = 0,
ntf = 2, ntc = 2, tol = 0.000001,
temp0 = 300, tempi = 300,
nstlim= 100,
ntpr = 1, ntwr = 100, ntwx = 100,
dt = 0.001,
cut = 999,
ntr = 0
/
&ewald
skinnb = 1.
/

mdout with SHAKE turn on

NSTEP = 0 TIME(PS) = 240.000 TEMP(K) = 358.59 PRESS =
0.0
Etot = 1251.2749 EKtot = 762.4585 EPtot =
488.8164
BOND = 160.6557 ANGLE = 409.9508 DIHED =
160.0572
1-4 NB = 166.0179 1-4 EEL = 0.0000 VDWAALS =
-407.8651
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------

NSTEP = 1 TIME(PS) = 240.001 TEMP(K) = 381.47 PRESS =
0.0
Etot = 1299.9308 EKtot = 811.1144 EPtot =
488.8164
BOND = 160.6557 ANGLE = 409.9508 DIHED =
160.0572
1-4 NB = 166.0179 1-4 EEL = 0.0000 VDWAALS =
-407.8651
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------

NSTEP = 2 TIME(PS) = 240.002 TEMP(K) = 372.36 PRESS =
0.0
Etot = 1276.6661 EKtot = 791.7429 EPtot =
484.9232
BOND = 157.0308 ANGLE = 409.3685 DIHED =
161.0973
1-4 NB = 167.0402 1-4 EEL = 0.0000 VDWAALS =
-409.6137
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------

NSTEP = 3 TIME(PS) = 240.003 TEMP(K) = 309.78 PRESS =
0.0
Etot = 1135.4141 EKtot = 658.6802 EPtot =
476.7340
BOND = 150.5532 ANGLE = 407.3157 DIHED =
161.8524
1-4 NB = 166.5745 1-4 EEL = 0.0000 VDWAALS =
-409.5619
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------

NSTEP = 4 TIME(PS) = 240.004 TEMP(K) = 313.99 PRESS =
0.0
Etot = 1135.2596 EKtot = 667.6442 EPtot =
467.6154
BOND = 144.9528 ANGLE = 404.5157 DIHED =
162.2624
1-4 NB = 165.5081 1-4 EEL = 0.0000 VDWAALS =
-409.6235
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------

NSTEP = 5 TIME(PS) = 240.005 TEMP(K) = 317.53 PRESS =
0.0
Etot = 1135.1592 EKtot = 675.1604 EPtot =
459.9987
BOND = 141.6399 ANGLE = 401.7405 DIHED =
162.3934
1-4 NB = 164.0167 1-4 EEL = 0.0000 VDWAALS =
-409.7917
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
...............................

mdout without SHAKE.( mdin file is similar with the above one but ntf=ntc=1)

NSTEP = 0 TIME(PS) = 240.000 TEMP(K) = 299.87 PRESS =
0.0
Etot = 1454.6407 EKtot = 762.4585 EPtot =
692.1822
BOND = 364.0215 ANGLE = 409.9508 DIHED =
160.0572
1-4 NB = 166.0179 1-4 EEL = 0.0000 VDWAALS =
-407.8651
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------

NSTEP = 1 TIME(PS) = 240.001 TEMP(K) = 299.87 PRESS =
0.0
Etot = 1454.6407 EKtot = 762.4585 EPtot =
692.1822
BOND = 364.0215 ANGLE = 409.9508 DIHED =
160.0572
1-4 NB = 166.0179 1-4 EEL = 0.0000 VDWAALS =
-407.8651
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------

NSTEP = 2 TIME(PS) = 240.002 TEMP(K) = 309.22 PRESS =
0.0
Etot = 1452.4437 EKtot = 786.2362 EPtot =
666.2075
BOND = 337.3843 ANGLE = 409.4576 DIHED =
161.2088
1-4 NB = 166.4308 1-4 EEL = 0.0000 VDWAALS =
-408.2740
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------

NSTEP = 3 TIME(PS) = 240.003 TEMP(K) = 327.58 PRESS =
0.0
Etot = 1447.9309 EKtot = 832.9152 EPtot =
615.0157
BOND = 288.2540 ANGLE = 407.6504 DIHED =
161.9261
1-4 NB = 166.3070 1-4 EEL = 0.0000 VDWAALS =
-409.1219
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------

NSTEP = 4 TIME(PS) = 240.004 TEMP(K) = 331.97 PRESS =
0.0
Etot = 1447.6689 EKtot = 844.0807 EPtot =
603.5883
BOND = 281.0537 ANGLE = 404.7102 DIHED =
162.3081
1-4 NB = 165.6109 1-4 EEL = 0.0000 VDWAALS =
-410.0946
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------

NSTEP = 5 TIME(PS) = 240.005 TEMP(K) = 320.78 PRESS =
0.0
Etot = 1451.9056 EKtot = 815.6143 EPtot =
636.2913
BOND = 319.0905 ANGLE = 401.3894 DIHED =
162.4341
1-4 NB = 164.3890 1-4 EEL = 0.0000 VDWAALS =
-411.0117
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------

NSTEP = 6 TIME(PS) = 240.006 TEMP(K) = 315.01 PRESS =
0.0
Etot = 1454.1888 EKtot = 800.9527 EPtot =
653.2361
BOND = 340.8348 ANGLE = 399.0163 DIHED =
162.3436
1-4 NB = 162.7577 1-4 EEL = 0.0000 VDWAALS =
-411.7163
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------

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Received on Tue Oct 18 2005 - 06:53:00 PDT
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