it sounds like your parameters are messed up somehow.
work on a very small model system to sort it out... just the new
residue?
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
===================================================================
Stern, Julie wrote:
>Hello Amber-onians,
>
> What does vlimit exceeded usually mean? I lowered dt from .005 to .001
>and
>went from a molecule that was blowing apart to a molecule that stays intact
>but
>ends up looking like spagetti with parts of the molecule bending and folding
>in
>on itself (out of what I thought would be a bending range) and atoms trying
>to
>occupy the same location. The temperature is blowing up. I have made my
>own
>residue and therefore had to add my own bond, angle, and dihedral
>information.
> I've attached the minimization output, the equilibration sanders
>program, and
>the equilibration output where the vlimit is exceeded after the first time
>step,
>and dihedral info.
> Does anything look blatently wrong in this info? What should values of
>GMAX
>be in order to be considered acceptable? What would cause a temperature
>blow up?
>Any suggestions of what to look for or try?
>
> Thanks.
>
>--Julie
>
>
>Output from minimization:
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3990 5.5483E+02 2.5547E-01 1.2457E+01 C1 1902
>
> BOND = 86.2263 ANGLE = 228.9414 DIHED =
>287.3746
> VDWAALS = -633.1069 EEL = 4565.9321 HBOND =
>0.0000
> 1-4 VDW = 714.9689 1-4 EEL = -4695.5047 RESTRAINT =
>0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 4000 5.5476E+02 1.9078E+00 5.7553E+01 C1 2152
>
> BOND = 86.2097 ANGLE = 229.6743 DIHED =
>287.4078
> VDWAALS = -633.3899 EEL = 4566.0074 HBOND =
>0.0000
> 1-4 VDW = 714.7744 1-4 EEL = -4695.9249 RESTRAINT =
>0.0000
>
>equilibration program:
>
> &cntrl
> imin = 0,
> ntx = 1, ntb = 1,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 150000, dt = 0.001,
> ibelly = 1, bellymask = "!.SA",
> ntpr = 1, ntwx = 100, ntwr = 1000,
> cut = 8, ntr=0,
>
>Output from equilibration:
>
> &end
> NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 301.73 PRESS =
>0.0
> Etot = 2670.1410 EKtot = 2115.3822 EPtot =
>554.7587
> BOND = 86.2097 ANGLE = 229.6742 DIHED =
>287.4078
> 1-4 NB = 714.7744 1-4 EEL = -4695.9249 VDWAALS =
>-633.3899
> EELEC = 4566.0074 EHBOND = 0.0000 RESTRAINT =
>0.0000
> Ewald error estimate: 0.2691E-02
>
>----------------------------------------------------------------------------
>--
>
> vlimit exceeded for step 1 ; vmax = 25.6763665728572
>
> NSTEP = 2 TIME(PS) = 0.002 TEMP(K) = 4005.60 PRESS =
>0.0
> Etot = 30518.1593 EKtot = 28082.5223 EPtot =
>2435.6370
> BOND = 248.0453 ANGLE = 283.2616 DIHED =
>1952.3529
> 1-4 NB = 717.1111 1-4 EEL = -4699.9718 VDWAALS =
>-632.4617
> EELEC = 4567.2997 EHBOND = 0.0000 RESTRAINT =
>0.0000
> Ewald error estimate: 0.2645E-02
>
>
>Dihedral info from frcmod file:
>
>DIHE
>SA-CT-CT-CT 1.100 180.000 2.
>SA-CT-CT-HC 1 0.250 0.000 1.
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber.scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Feb 22 2005 - 16:53:02 PST
