AMBER Archive (2004)

Subject: Re: AMBER: strange output of MD

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Jan 07 2004 - 11:57:13 CST

> I have just built up a small molecule. And I ran the
> Minimization first and then MD as usual. ...
> this time the MD output is strange
>
> [min.out]
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 2.3391E+04 3.2374E+04 2.0326E+05 O30 11
> BOND = 0.0023 ANGLE = 12.3206 DIHED = 4.3342
> VDWAALS = 23565.9892 EEL = -289.6052 HBOND = 0.0000
> 1-4 VDW = 9.2099 1-4 EEL = 88.7886 RESTRAINT = 0.0000
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 622 -1.2307E+02 4.4446E-04 1.6950E-03 OS3 30
> BOND = 4.4854 ANGLE = 27.1946 DIHED = 9.3549
> VDWAALS = 2.6568 EEL = -227.1559 HBOND = 0.0000
> 1-4 VDW = 6.4332 1-4 EEL = 53.9580 RESTRAINT = 0.0000
>
> md.in :
> ...
> tempi = 300.0, temp0 = 300.0, ntt = 1, tautp = 0.5,
>
> [md.out]
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 512.36 PRESS = 0.0
> Etot = 23429.7296 EKtot = 38.6900 EPtot = 23391.0395
> BOND = 0.0023 ANGLE = 12.3206 DIHED = 4.3342
> 1-4 NB = 9.2099 1-4 EEL = 88.7886 VDWAALS = 23565.9892
> EELEC = -289.6052 EHBOND = 0.0000 RESTRAINT = 0.0000

BOND at the end of minimization is 4.4854, but at the beginning of
dynamics it is 0.0023 - the same as at the beginning of minimization.
Apparently you are not using your min restrt file as input for MD.

Also cold-starting to 300K can be a problem, especially when the
molecule has not been minimized. (Small molecules can often be
successfully cold-started, depends on size and structure.)

Bill Ross

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