Dear Grzegorz,
>From your output it looks as though you set irest=0 and ntx=1 in the 2nd
run. The first run dyn0.out did have pressure control (ntp=1) and the
density went up from 0.92 to ~1. When you restart, unless you set ntx=7
the periodic cell size will be the same as at the start of dyn0. Thus the
density at 1 step was back at 0.92. So, most likely the box dimensions
were inappropriate for the second run.
Also, in pme don't necessarily worry about waters escaping. The periodic
boundary conditions are still enforced internally i.e. that water has an
image inside the box and so the system feels it as if it were there.
In brief, set ntx=7 and irest=1 when you restart so that the box size and
temperature are as they were at the end of previous run.
Hope this helps
Tom Darden
On Mon, 18 Dec 2000, Grzegorz Jezierski wrote:
> Dear AMBER users,
>
> I had performed 20 ps-MD of a 78000 atom system.
> I used PBC, no pressure control, and PME.
> Then, I have restarted the calculation, and got (after 1 MD iteration) a
> message, like:
> "Ewald bomb in subroutine 'ewald_list'
> volume of ucell too big"
> At the first sight, the solute structure (protein) seems OK, but several water
> molecules 'flew out' of the box.
> I attach the output file from the last - unfinished - run ('dyn.out') as well as
> the beginning and the end of the previous run ('dyn0.out').
> Thank you for any help.
>
> Regards,
> --
> ********************************
> Grzegorz Jezierski
>
> Biophysics Department
> Institute of Molecular Biology
> Jagiellonian University
> al. Mickiewicza 3, 31-120 Krakow
> ph.:(48 12)6341305 ext.291
> e-mail: gj_at_mol.uj.edu.pl
> ********************************
>
Received on Mon Dec 18 2000 - 15:20:43 PST
