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

From: case <case.biomaps.rutgers.edu>
Date: Mon, 2 Apr 2012 21:19:27 -0400

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 integers.

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 been
tested for. I'm assuming that you aren't running atomic or molecular
simulations (one could put about 22 million water molecules into a 900x900x900
box, and I'm pretty sure nothing in our codes would work at that size limit.)
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 and
find the origin of segfaults on your own.

...good luck....dac


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 02 2012 - 18:30:04 PDT
Custom Search