Hi, all,
I followed the tutorial 1 and the tutorial of non-standard residue, and i
did try to simulate only the hydrogen molecule with explicit water and it
was fine as well :(
Any other suggestions, now i really dont know where shall i start to solve
the problem ::>_<:: any suggestion will be greatly appreciated.
best regards,
Rachel
On 11/10/06, Carlos Simmerling <carlos.csb.sunysb.edu> wrote:
>
> 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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> >
> >
>
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Received on Sun Nov 12 2006 - 06:07:35 PST
