On Tue, Dec 16, 2014, 杨川 wrote:
> I am trying to simulate a protein with drug. First i use
> minimize the Protein and drug only. Then i minimize the
> whole system( Protein+drug+water box). After this i heated
> the Protein from 0K to 300K. Then i want to equilabrate
> the complex but it gives me the Following error. I checked
> it on CPU but it gives the same error. kindly give me some
> comments.
> "ERROR: Calculation halted. Periodic box dimensions have changed too
> much from their initial values.
> Your system density has likely changed by a large amount, probably from
> starting the simulation from a structure a long way from equilibrium.
>
> [Although this error can also occur if the simulation has blown up for some reason]
>
First, of course, do what is suggested: restart the calculation (on the CPU)
from the last restart.
Also, run a shorter constant pressure simulation, and print every 10 steps or
so. Is your density changing rapidly? You didn't really say (or I missed it)
how you created the initial water box. It *might* help to use a much longer
value of taup, say 100ps (just for the equilibration). If you can't figure it
out, please describe how you created the initial system, and what the density
is near the beginning of the constant pressure simulation, or whenever the
system stops with the above message.
....dac
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Received on Tue Dec 16 2014 - 05:30:03 PST
