[gmx-developers] RE: no pull

Justin MacCallum jlmaccal at ucalgary.ca
Sat Feb 21 18:31:29 CET 2004


I actually didn't realize that g_wham was still even part of the
distribution. As far as I'm concerned, this can be removed for the next
release. So Erik, David, or Berk could you please remove g_wham from CVS?

Michael, I recieved your earlier email regarding a potential bug, but I've
been in Baltimore for the Biophysical Society meeting for the last week.
I'll look into your suggested fix, and try to do some testing. If you could
try the fix that Berk proposed and report back, that would save some time.


> two issues:
> 1) g_wham that comes with gmx-3.2 can not read
> pull.pdo files produced by gmx-3.2
> 2) In the umbrella sampling code in pull.c there is
> a subroutine do_umbrella containing a function put_dvec_in_box.
> This function is appearently meant to account for periodic
> boundary conditions when calculating the distance between
> the reference and the pull group. This function does not
> do what it was intended to do. I believe this is a bug.
> (umbrella sampling only gives reasonable results when
>  a) this funtion is commented out, and
>  b) (maybe ?) the pulled group does not cross a cell boundary.)
> please let me know if updated versions of the code are available
> somewhere!
> cheers,
> Michael

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