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Per Larsson

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03/18/2013

03:21 PM GROMACS Bug #1194 (Closed): Dihedral restraints in 4.5.X vs 4.6
This is about starting simulation from a 4.5.5 tpr-file using 4.6 (or 4.6.1) that contains dihedral restraints.
I h...

10/28/2010

08:44 PM GROMACS Revision c09840c8: Fixed a bug in the all-vs-all sse gb kernels, where an exclusion mask was
calculated incorrectly. Also fixes to loop indeces in the all-vs-all non-sse
code.

10/22/2010

10:33 AM GROMACS Bug #599: mdrun minimization crashes with GBSA / HCT and virtual site
Fixed by adding a check to grompp that covers the case with all GB-parameters set to zero while at the same time havi...
10:31 AM GROMACS Revision 8a95cc08: Added a check in grompp for the case with particles having a non-zero
charge while all GB-parameters are set to zero. This fixes bug #599.

10/21/2010

07:43 PM GROMACS Bug #599: mdrun minimization crashes with GBSA / HCT and virtual site
Hi!
The reason for this crash is your ET-vsite.
You have set the gb-parameters all to zero, while ET is also having ...
09:15 AM GROMACS Bug #599: mdrun minimization crashes with GBSA / HCT and virtual site
What forcefield did you use?
Since you have the ligand MOL in their, I suspect that is where things go wrong
Could yo...

10/20/2010

10:30 PM GROMACS Bug #599: mdrun minimization crashes with GBSA / HCT and virtual site
Hi!
Could you please provide me with your input .gro and .mdp - files, to speed the resolution of this bug.
Thanks!
10:45 AM GROMACS Bug #585: results of double precision GBSA em drastically change with number of threads
Energies were summed incorrectly in double precision SSE-loops.
The reason was that _mm128d _mm_add_sd(a,b) which sho...
09:07 AM GROMACS Revision c83f1f38: Removed code for calculating logarithms using a table
This was not much faster than the builtin c-function,
and also only used in the non-sse loops

10/19/2010

10:32 AM GROMACS Revision 81ce3c32: Fixed a compiler warning introduced by commit 9ccc786e4...

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