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.
Thanks in advance!
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
------------------------------------------------------------------------------
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Oct 18 2005 - 06:53:00 PDT
