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

From: Pengzhi <>
Date: Mon, 2 Apr 2012 21:59:58 -0500

On Mon, Apr 02, 2012, Pengzhi wrote:
> I have a system with PBC. The dimension of the cubic box I use is 900? *
> 900? * 900?. When I set the cut-off to be 450? or slightly less than that,
> my system ends up with explosion. I have the error message:
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> I can avoid this by setting a smaller cutoff (anything smaller than 360?
> works). However, if I want to keep as much interactions as possible,
> technically what is up limit of the cut-off in amber10 given size of the
> box?

There could be all sorts of things that fail, including the non-bonded list
generation, and many other things, since Amber is built with 32-bit

You don't say whether you are using sander or pmemd, nor how many atoms you
have. You may be way outside the range that Amber was written for, or has
tested for. I'm assuming that you aren't running atomic or molecular
simulations (one could put about 22 million water molecules into a
box, and I'm pretty sure nothing in our codes would work at that size
We've never even considered interactions that would operate on the length
scales you are describing.

Bottom line, you probably are going to have to learn how to use a debugger
find the origin of segfaults on your own.

...good luck....dac
Thanks for your reply, dac.

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?

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Received on Mon Apr 02 2012 - 20:30:03 PDT
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