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> 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
