Hi All,
We are seeing more and more examples on the GPU code of calculations
crashing due to zero VDW radii on Hydrogens. This is becoming more and
more of a problem as we move to longer and longer time scales. Please take
a look at the following bug report:
http://bugzilla.ambermd.org/show_bug.cgi?id=180
Specifically the last comment.
-----
Just hacked the VDW parameters for the hydrogens to 0.0000001.
Marking this as resolved. We need to fix the force field - the code is
fine.
Lachele, if you can find a case where the VDW radii are non-zero, re-open
the
bug
and send it to me. Otherwise, we're done here.
Ross, you could put a warning about this in the FORTRAN code since it's no
gpu-specific, but I really think the solution is to not entirely zero out
the
VDW radii.
-----
So I am proposing that we have code in rdparm that detects zero VDW radii,
prints a warning message about it and then adjusts these radii in the code
to 0.0000001.
Objections, comments / other solutions?
Should we do this inside the force field parm files instead? - Or have
leap write 0.0000001 instead of 0?
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Associate Research Professor |
| San Diego Supercomputer Center |
| Adjunct Associate Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Fri Aug 16 2013 - 10:30:03 PDT
