Yufeng,
Yes, this is due to the lack of main memory on your computer. Can you
try to double the grid spacing (space) and try again? Doing so would
reduce the memory usage by a factor of 8. If it works, you can try a
number less aggressive.
All the best,
Ray
On Mon, Jul 8, 2013 at 1:34 AM, crazylyf <crazylyf.126.com> wrote:
> Hi everybody,
>
> I'm trying to estimate the free energy evolution of a membrane protein from trajectory, using PBSA implicit membrane and solvent in sander (version AmberTools12). After solved several problems, I finally got stuck with such an error:
> "SA Bomb in sa_arc()3: Allocates aborted 5014 5014 5014 5014 5014"
>
> I noticed that previous discussions in the archive pointed out that it may be caused by the lack of memory, and suggested to increase the arcres. However, my calculation still failed with arcres 0.125, 0.25, or even larger. I also tried to split the trajectory into small small pieces, but they aborted quickly again.
>
> Could anyone tell me what is going on? Thanks in advance!
>
> Best,
>
> Yufeng
>
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Received on Mon Jul 08 2013 - 10:30:02 PDT
