Julie,
did you minimize the structure first? If so, look at the end of the min.out
at the gradient info to see if any atoms had high forces.
you might want to also post your sander input file.
carlos
Stern, Julie wrote:
>+Amber Users,
> My molecule which contains 1 new atom and is made up of 1 new residue
>repeated
>in a lattice is blowing apart at the equilibrium stage. The output of the
>equilibration
>follows. Is it obvious which parameter blows up first? Can anything be
>told
>from this equilibration output?
> Are there general reasons why the atoms would all separate from each
>other?
>The data in the frcmod file that I assigned are ballpark with other similar
>parameters/molecules, so even if they were slightly off, it shouldn't cause
>a blow up. The minimization energy prior to this looked reasonable.
> What kinds of things should I check in this type of problem?
>
>Thanks.
>--Julie
>
>
>| Local SIZE OF NONBOND LIST = 1903418
>| TOTAL SIZE OF NONBOND LIST = 1903418
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 304.28 PRESS =
>0.0
> Etot = -22104.6357 EKtot = 4222.0829 EPtot =
>-26326.7187
> BOND = 144.4108 ANGLE = 422.0464 DIHED =
>566.4332
> 1-4 NB = 1568.3971 1-4 EEL = -9231.7817 VDWAALS =
>-2585.5964
> EELEC = -17210.6281 EHBOND = 0.0000 RESTRAINT =
>0.0000
>
>----------------------------------------------------------------------------
>--
>
>
> NSTEP = 1 TIME(PS) = 0.005 TEMP(K) = 304.17 PRESS =
>0.0
> Etot = -22106.2294 EKtot = 4220.4893 EPtot =
>-26326.7187
> BOND = 144.4108 ANGLE = 422.0464 DIHED =
>566.4332
> 1-4 NB = 1568.3971 1-4 EEL = -9231.7817 VDWAALS =
>-2585.5964
> EELEC = -17210.6281 EHBOND = 0.0000 RESTRAINT =
>0.0000
>
>----------------------------------------------------------------------------
>--
>
> vlimit exceeded for step 1 ; vmax = 139.057814268365
>
> NSTEP = 2 TIME(PS) = 0.010 TEMP(K) = 12093.05 PRESS =
>0.0
> Etot = 171734.3247 EKtot = 167797.8906 EPtot =
>3936.4341
> BOND = 7973.0844 ANGLE = 3071.4581 DIHED =
>16280.2842
> 1-4 NB = 1705.3258 1-4 EEL = -9280.7139 VDWAALS =
>-2431.5576
> EELEC = -13381.4469 EHBOND = 0.0000 RESTRAINT =
>0.0000
>
>----------------------------------------------------------------------------
>--
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Received on Fri Feb 18 2005 - 20:53:01 PST
