Re: [AMBER] A problem about periodic box dimensions happens to Tutorial 1.7

From: David A Case <>
Date: Mon, 6 Sep 2021 16:27:50 -0400

On Sun, Sep 05, 2021, wangwei1669 wrote:
>I don't know why there are larger density and smaller volume recorded after
>600 ps than those at 105 ps. I see the systems dramatically enlarging after
>105 ps (hold and production).

This is because your initial density is much lower than the system wants,
and commonly is seen in water simulations, depending on exactly how you
added water to the system. Once the water gets to about the right density,
there are no futher changes.

>And I also concern that I sourced ff14SB force field instead of ff12SB
>that used in tutorial web since I did not find it. Does this significantly
>influence the result?

This should make no difference. ff14SB is the "final" version of this force
field, whereas ff12SB was an intermediate version, but very close (I think)
to the final version

>>>The simulation stopped at 80 ns and I received a feedback:
>>>"ERROR: Calculation halted. Periodic box dimensions have changed too much
>>>from their initial values.

As I said, it is unusual to have a simulation halt in this way during the
middle of a run...or did you get this message near the beginning of a
restart? You could look not just at the average density over the whole 80
ns, but rather at the behavior right before the crash. You may need to
re-run a simulation with a slightly shorter time (before the time of the
crash), then see if you have problems when restarting. What you are trying
to get is a way to reproduce the crash without needing a long simulation.
That would be the first step to tracking down what is going on.


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Received on Mon Sep 06 2021 - 13:30:03 PDT
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