Re: [AMBER] Setting the cut-off and size of box

From: case <>
Date: Tue, 3 Apr 2012 22:53:48 -0400

On Mon, Apr 02, 2012, Pengzhi wrote:
> Sorry for missing of information. I'm using sander, and the system is quite
> simple and the number of atoms is about 800. I stated that the simulation
> can go with a smaller cutoff, which may help exclude other reasons to have
> the system blown up.
> You were not answering my question about setting the cutoff....... Ignoring
> the error message I got, is there an exact up limit for the cutoffs given
> the box size? Or it depends from case to case?

The "ordinary" limit is that twice the cutoff plus skinnb cannot be bigger than
the smallest box dimension. But exceeding this should just lead to a regular
error message, not to a segfault.

If you have 800 "atoms" in a 900x900x900 box you are way,way outside the range
of anyone's experience with Amber. I'm pretty sure no one on the list could
tell what is causing your segfault (which has no intrinsic information, other
than that something went wrong). The configure script has a "-debug" flag,
which should get you started in the right direction.

....good luck....dac

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Received on Tue Apr 03 2012 - 20:00:03 PDT
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