On Tue, Mar 25, 2008, James Thomas wrote:
>
> I am running a nmode program using amber9 package. I tried using a smaller
> file as a test (the prmtop size: 566999 & the inpcrd: 50451). My interest
> protein has this (the prmtop size: 2307687 & the inpcrd size:210978).
> However, I got the error message of segmentation fault few minutes after I
> started the run.
It is much more helpful to know how many atoms you have in each case; the
size of the prmtop file itself is not very informative.
>
> My test run using test protein is successful to complete 100 steps of Newton
> minimization.
This sounds suspicious: Newton Raphson should generally converge in much less
than 100 steps. (You should have done a lot of CG minimization before
starting NR.)
>
> I also refer this : http://amber.scripps.edu/bugfixes/6.0/bugfix.28, but not
> sure on how to modify the alloc.f file.
This is about amber 6(!). Should be completely irrelevant for Amber 9.
>
> Is that because my protein of interest is too big?
See above...dac
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Received on Fri Apr 18 2008 - 21:13:57 PDT
