AMBER Archive (2004)

Subject: Re: AMBER: strange output of MD

From: L Jin (s0344557_at_sms.ed.ac.uk)
Date: Wed Jan 07 2004 - 12:21:03 CST

Thank you Bill. It really does matter with the restrt from minimization as input
for MD.

But I am still confused that I once used just the crd file instead of the restrt
from minimization as input for MD and the output of the MD was correct. And the
two molecule size are the same. Then why one is OK while the other fails? Would
you please give some suggestion?

Lan

Quoting Bill Ross <ross_at_cgl.ucsf.edu>:

> > 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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