On Sat, Nov 22, 2014, Hadeer ELHabashy wrote:
>
> I want to run MD simulation for a protein in a TIP3P water box with
> average 7100 atoms for 20 ns with step length of 0.001 ps. I am using NPT
> ensemble with Langevin dynamics and periodic boundary conditions. After 6
> ns of mds the run stopped with the following error " peek_ewald_inpcrd:
> SHOULD NOT BE HERE <http://archive.ambermd.org/201103/0197.html>"
I'm assuming that you completed one or more runs, and then were at the
beginning of a restart, since the error you mention should only happen
at the very beginning of a run.
It looks like there is something wrong with the the input coordinate (restart)
file you are using, but we don't have enough information to say more. Look
at the the size of that last restart file, compared to any earlier ones.
See if there are any "*" characters inside it.
One other possibility: the input coordinate file is not a restart file:
perhaps it came from a minimization (and hence has no velocities), or is
otherwise mis-named.
> nstlim=5000, nscm=500, nrespa=1,
Aside: is this small value of nstlim just from a test run? Ordinarily, one
would not think of dividing a 20 ns run into 5 ps pieces....
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Nov 22 2014 - 12:00:02 PST
