AMBER Archive (2005)

Subject: Re: AMBER: Question about NVE simulation.

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Tue Oct 18 2005 - 07:02:39 CDT

you assigned it random initial velocities, and some of them are along the
vectors that you constrain with SHAKE, which will remove it.
When you use ntf=2 you tell sander not to calculate those
energies. Try ntf=1 and see if the energy of the bonds changes.

tanc_at_uci.edu wrote:

>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
> ------------------------------------------------------------------------------
>
>
>
>
>
>
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