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.
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Received on Tue Feb 22 2005 - 16:53:02 PST
