Hi.
I would like to know more details about the way AMBER7 calculates the
non-bonded interactions.
I work with ntb = 0 ( no periodicity althoug I have used the
SolvateCap WATBOX216 option in xleap ), and it seems to me that despite
this direct sum nonbonded list from ewald calculations are used. I
don`t understand why at the end of the mdout file appears:
| Read coords time 0.10 ( 0.07% of Total)
| Ewald setup time 0.04 ( 1.89% of List )
| Check list validity 1.53 (72.17% of List )
| Grid unit cell 0.24 (11.32% of List )
| Grid image cell 0.02 ( 0.94% of List )
| Build the list 0.27 (12.74% of List )
| Other 0.02 ( 0.94% of List )
| List time 2.12 ( 1.71% of Nonbo)
| Direct Ewald time 119.89 (98.29% of Ewald)
| Finish NB virial 1.17 ( 0.96% of Ewald)
| Other 0.92 ( 0.75% of Ewald)
| Ewald time 121.98 (98.27% of Nonbo)
| Other 0.03 ( 0.02% of Nonbo)
| Nonbond force 124.13 (96.90% of Force)
| Bond energy 1.28 ( 1.00% of Force)
| Angle energy 0.05 ( 0.04% of Force)
| Dihedral energy 0.05 ( 0.04% of Force)
| Noe calc time 0.02 ( 0.02% of Force)
| Other 2.57 ( 2.01% of Force)
because I work with no periodicity. ( The same if I set nbflag = 0 )
Could anybody tell me what`s happening?
Thanks in advance
Received on Tue Jul 30 2002 - 07:41:49 PDT
