On Wed, Sep 29, 2010, nicholus bhattacharjee wrote:
> I am running some constant pH MD simulation at pH
> 1,3,5,9. For pH 1,3,9 i could do the simulation upto 3 nano seconds. But for
> pH 5
> after 319 pico seconds following error is given in output file
>
>
>
> NSTEP = 159500 TIME(PS) = 319.000 TEMP(K) = 300.11 PRESS =
It looks like you may be running with a time step of 0.002(?) See if cutting
that in half helps. I know that people claim to "get away with" a time step
of 0.002 for GB simulations, but to me that seems very close to the edge (or
over the edge) of stability. [This is not so much a problem with explicit
solvent simulations, where one has lots of collisions.]
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 29 2010 - 12:00:07 PDT
