my guess is that there is a problem in the parameters
that you added. that can be a very difficult thing to do
and to debug. did you follow the tutorials? is the new
molecule something that you can simulate alone to see if
it is ok?
Rachel wrote:
> Hi, all,
>
> As David suggested, I ran a short (2ps) MD with the same ntf, ntc
> parameters used for minimization, and used the .rst files from the
> minimization, and this time, the job did finish but with a lot of
> 'vlimit exceeded for step 0 (1,2,....) ; vmax = Infinity', and at the
> 0 step, all the energy terms are the same as the last step of the
> minimization. And from the results, the bond energy kept increasing,
> from ~13557 to ~29159, and the Etot increased during this run as well.
>
> Here is the 0 step output:
> -----------------------------------------------------------------------------------------------------------------
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS
> = 0.0
> Etot = -201927.6502 EKtot = 0.0000 EPtot =
> -201927.6502
> BOND = 13557.7749 ANGLE = 2100.0258 DIHED =
> 6683.4797
> 1-4 NB = 2495.1800 1-4 EEL = 33508.5993 VDWAALS =
> 24316.5978
> EELEC = -284589.3078 EHBOND = 0.0000 RESTRAINT
> = 0.0000
>
> vlimit exceeded for step 0 ; vmax = Infinity
> vlimit exceeded for step 1 ; vmax = Infinity
> vlimit exceeded for step 2 ; vmax = Infinity
> vlimit exceeded for step 3 ; vmax = Infinity
> vlimit exceeded for step 4 ; vmax = Infinity
> vlimit exceeded for step 5 ; vmax = Infinity
> vlimit exceeded for step 6 ; vmax = Infinity
> vlimit exceeded for step 7 ; vmax = Infinity
> vlimit exceeded for step 8 ; vmax = Infinity
> vlimit exceeded for step 9 ; vmax = Infinity
> vlimit exceeded for step 10 ; vmax = Infinity
> vlimit exceeded for step 11 ; vmax = Infinity
> vlimit exceeded for step 12 ; vmax = Infinity
> vlimit exceeded for step 13 ; vmax = Infinity
> vlimit exceeded for step 14 ; vmax = Infinity
> vlimit exceeded for step 15 ; vmax = Infinity
> vlimit exceeded for step 16 ; vmax = Infinity
> vlimit exceeded for step 17 ; vmax = Infinity
> vlimit exceeded for step 18 ; vmax = Infinity
> vlimit exceeded for step 19 ; vmax = Infinity
>
> NSTEP = 20 TIME(PS) = 0.020 TEMP(K) = 8.08 PRESS
> = 0.0
> Etot = -199277.8331 EKtot = 1348.4210 EPtot =
> -200626.2541
> BOND = 14419.0582 ANGLE = 2231.5310 DIHED =
> 6701.6667
> 1-4 NB = 2498.6373 1-4 EEL = 33492.7200 VDWAALS =
> 24465.0565
> EELEC = -284439.3857 EHBOND = 0.0000 RESTRAINT
> = 4.4619
> EAMBER (non-restraint) = -200630.7160
> Ewald error estimate: 0.1356E-03
> vlimit exceeded for step 20 ; vmax = Infinity
> vlimit exceeded for step 21 ; vmax = Infinity
> vlimit exceeded for step 22 ; vmax = Infinity
> vlimit exceeded for step 23 ; vmax = Infinity
> vlimit exceeded for step 24 ; vmax = Infinity
> vlimit exceeded for step 25 ; vmax = Infinity
> vlimit exceeded for step 26 ; vmax = Infinity
> vlimit exceeded for step 27 ; vmax = Infinity
> vlimit exceeded for step 28 ; vmax = Infinity
> vlimit exceeded for step 29 ; vmax = Infinity
> vlimit exceeded for step 30 ; vmax = Infinity
> vlimit exceeded for step 31 ; vmax = Infinity
> vlimit exceeded for step 32 ; vmax = Infinity
> vlimit exceeded for step 33 ; vmax = Infinity
> vlimit exceeded for step 34 ; vmax = Infinity
> vlimit exceeded for step 35 ; vmax = Infinity
> vlimit exceeded for step 36 ; vmax = Infinity
> vlimit exceeded for step 37 ; vmax = Infinity
> vlimit exceeded for step 38 ; vmax = Infinity
> vlimit exceeded for step 39 ; vmax = Infinity
>
> ----------------------------------------------------------------------------------
>
> And here is the output of the last 20 steps:
>
> ------------------------------------------------------------------------------------------------------------------
>
> NSTEP = 1980 TIME(PS) = 1.980 TEMP(K) = 260.64 PRESS
> = 0.0
> Etot = -118308.7362 EKtot = 43484.3597 EPtot =
> -161793.0959
> BOND = 29110.4092 ANGLE = 6066.9933 DIHED =
> 7593.6930
> 1-4 NB = 2769.3148 1-4 EEL = 33369.0797 VDWAALS =
> 22569.8911
> EELEC = -264113.6787 EHBOND = 0.0000 RESTRAINT =
> 841.2016
> EAMBER (non-restraint) = -162634.2975
> Ewald error estimate: 0.2381E-05
> vlimit exceeded for step 1980 ; vmax = Infinity
> vlimit exceeded for step 1981 ; vmax = Infinity
> vlimit exceeded for step 1982 ; vmax = Infinity
> vlimit exceeded for step 1983 ; vmax = Infinity
> vlimit exceeded for step 1984 ; vmax = Infinity
> vlimit exceeded for step 1985 ; vmax = Infinity
> vlimit exceeded for step 1986 ; vmax = Infinity
> vlimit exceeded for step 1987 ; vmax = Infinity
> vlimit exceeded for step 1988 ; vmax = Infinity
> vlimit exceeded for step 1989 ; vmax = Infinity
> vlimit exceeded for step 1990 ; vmax = Infinity
> vlimit exceeded for step 1991 ; vmax = Infinity
> vlimit exceeded for step 1992 ; vmax = Infinity
> vlimit exceeded for step 1993 ; vmax = Infinity
> vlimit exceeded for step 1994 ; vmax = Infinity
> vlimit exceeded for step 1995 ; vmax = Infinity
> vlimit exceeded for step 1996 ; vmax = Infinity
> vlimit exceeded for step 1997 ; vmax = Infinity
> vlimit exceeded for step 1998 ; vmax = Infinity
> vlimit exceeded for step 1999 ; vmax = Infinity
> check COM velocity, temp: 0.001738 0.00(Removed)
>
> NSTEP = 2000 TIME(PS) = 2.000 TEMP(K) = 261.62 PRESS
> = 0.0
> Etot = -118065.1346 EKtot = 43646.6434 EPtot =
> -161711.7780
> BOND = 29159.8896 ANGLE = 6078.2361 DIHED =
> 7553.8503
> 1-4 NB = 2814.0323 1-4 EEL = 33545.8687 VDWAALS =
> 22451.4667
> EELEC = -264153.8735 EHBOND = 0.0000 RESTRAINT =
> 838.7517
> EAMBER (non-restraint) = -162550.5297
> Ewald error estimate: 0.5605E-04
> ------------------------------------------------------------------------------
>
> A V E R A G E S O V E R 2000 S T E P S
>
>
> NSTEP = 2000 TIME(PS) = 2.000 TEMP(K) = 180.16 PRESS
> = 0.0
> Etot = -146151.3591 EKtot = 30057.4801 EPtot =
> -176208.8392
> BOND = 24202.5594 ANGLE = 4728.9371 DIHED =
> 7258.6396
> 1-4 NB = 2674.9284 1-4 EEL = 33448.8445 VDWAALS =
> 24842.9808
> EELEC = -273967.9303 EHBOND = 0.0000 RESTRAINT =
> 602.2015
> EAMBER (non-restraint) = - 176811.0407
> Ewald error estimate: 0.3811E-04
> ------------------------------------------------------------------------------
>
> And I tried to use this output, even it is obviously not correct, and
> changed the ntf, ntc values back to 2, and i got the same error
> message as before and the job stopped immediately.
>
> I really dont understand why this is happening, because for the
> exactly same protein i ran exactly the same jobs before and everything
> seemed to be OK, and the only difference in this system is that i
> added one hydrogen molecule which i built up myself into the system,
> and it started to complain about the vlimit.
>
> Any suggestions please? thanks a million in advance!
> Best regards,
>
> Rachel
>
> On 11/8/06, *David A. Case* <case.scripps.edu
> <mailto:case.scripps.edu>> wrote:
>
> On Wed, Nov 08, 2006, Rachel wrote:
> >
> > As can be seen, the bond energy changed from 13557.7748 to
> 396.4313 while
> > all other energies remained the same, is this happening because
> I changed
> > the ntc, ntf value from the minimization to the md?
>
> You should certainly try a short MD run with the same ntf,ntc
> parameters that
> you used for minimization. It looks like your minimization was
> trapped in
> a very bad local minimum (with a long bond length), so you will
> probably need
> to try to fix that problem as well.
>
> ...good luck...dac
>
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Received on Sun Nov 12 2006 - 06:07:34 PST
