It's not the same thing as my problem, but I think it might
be related to shake and your bonds to Fe.
At the end of minimization, the bond energy is 13557.,
really big. This is without shake I think.
Then you do MD with shake on H (ntc=2) and the
bond energy is 396. All of the other energy terms
are similar to the min output, so I would look into the
bonds. The gmax atom at the end of min is Fe, so
maybe it is bonds related to Fe? Did you add new
parameters for that?
carlos
Rachel wrote:
> Hi, Carlos,
>
> Thanks for your reply, the outputs are attached, the one crashed is
> named md1.out and the one right before it named min2.out. Thanks very
> much for your help!
>
> Rachel
>
>
> On 11/8/06, *Carlos Simmerling* <carlos.csb.sunysb.edu
> <mailto:carlos.csb.sunysb.edu>> wrote:
>
> I think I've seen this recently and I have some idea what
> might be happening but I need to run more tests and check
> the code. Can you send me your output files for the
> run that crashed and the run right before it? Send them
> directly so we don't clutter people's mail.
> thanks
> carlos
>
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> CMM Bldg, Room G80
> Stony Brook University E-mail:
> carlos.simmerling.stonybrook.edu
> <mailto:carlos.simmerling.stonybrook.edu>
> Stony Brook, NY 11794-5115
> ===================================================================
>
>
>
>
> Rachel wrote:
>
> > Hi, David,
> >
> > Thanks for your advice, i tried to change the tempi as well as
> the ntt
> > value as you suggested, however, both no luck, i still got the same
> > error message, and as I wrote in another email, i noticed that the
> > bond energy from the last step of minimization decreased
> dramatically
> > when I started to run the equilibration.
> >
> > Here is the output of the last step of the minimization:
> >
> ---------------------------------------------------------------------------------------------------------------
>
> >
> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> > 5000 -2.0193E+05 5.2652E-01 7.9133E+01
> FE 12110
> >
> > BOND = 13557.7748 ANGLE = 2100.0258 DIHED =
> > 6683.4797
> > VDWAALS = 24316.5978 EEL = -284589.3077 HBOND =
> > 0.0000
> > 1-4 VDW = 2495.1800 1-4 EEL = 33508.5993 RESTRAINT =
> > 0.0000
> >
> ------------------------------------------------------------------------------------------------------------------
>
> >
> > and here is the output of the equilibration of the system with
> > restraints on the solute:
> >
> >
> -------------------------------------------------------------------------------------------------------------------
>
> > | Local SIZE OF NONBOND LIST = 17919959
> > | TOTAL SIZE OF NONBOND LIST = 17919959
> >
> > NSTEP = 0 TIME(PS) = 0.000 TEMP(K) =
> 0.00 PRESS
> > = 0.0
> > Etot = - 215088.9939 EKtot = 0.0000 EPtot =
> > -215088.9939
> > BOND = 396.4313 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
> > Ewald error estimate: 0.1110E-03
> >
> > vlimit exceeded for step 0 ; vmax = Infinity
> >
> > Coordinate resetting (SHAKE) was not accomplished
> > within 3000 iterations
> >
> > Note: This is usually a symptom of some deeper
> > problem with the energetics of the system.
> >
> > ---------------------------------------------------------------------------------------------------------------------
> >
> > 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?
> >
> > Can anyone suggest how to solve this problem please?
> >
> > Thanks in advance!
> >
> > Rachel
> >
> >
> >
> >
> > On 11/8/06, *David A. Case* < case.scripps.edu
> <mailto:case.scripps.edu>
> > <mailto: case.scripps.edu <mailto:case.scripps.edu>>> wrote:
> >
> > On Wed, Nov 08, 2006, Rachel wrote:
> >
> > > vlimit exceeded for step 0 ; vmax = Infinity
> > >
> > > tempi = 0.0 ,
> > > temp0 = 300.0,
> > > ntt = 3,
> > > gamma_ln = 1.0,
> >
> > As a wild guess, try a short (10 step) simulation with tempi set
> > to some small
> > but non-zero value. It is possible that Langevin dynamics has
> > some bad
> > behavior when all the velocities are zero. Alternatively,
> try a short
> > simulation with ntt=1.
> >
> > This is shooting in the dark, but it is simple enough to be
> worth
> > a try.
> >
> > ...good luck....dac
> >
> >
> -----------------------------------------------------------------------
>
> >
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> >
> >
>
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Received on Sun Nov 12 2006 - 06:07:11 PST
