On Wed, Aug 14, 2019, Parviz Seifpanahi Shabane wrote:
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 9.6444E+06 1.9817E+02 2.3628E+05 N 14502
>
> BOND = 11548100.3201 ANGLE = 6025.3459 DIHED = 16671.4002
> VDWAALS = 260779.4630 EEL = -2201179.5517 HBOND = 0.0000
> 1-4 VDW = 7609.4364 1-4 EEL = 6393.5497 RESTRAINT = 0.0190
> EAMBER = 9644399.9636
You bond energy is suspicously high. Use the "checkValidity" action in parmed
(or the "checkstructure" action in cpptraj) to check for bad bond lengths.
Second, you minimized for only 20 steps, but with such a terrible starting
structure, this is not nearly enough to use as a starting point for MD.
It may be that more minimization will help, but you should really figure out
why your starting structure has such bad bonds.
....good luck....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 14 2019 - 18:30:04 PDT
