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- 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.
- 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
- 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.
- 07:43 PM GROMACS Bug #599: mdrun minimization crashes with GBSA / HCT and virtual site
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
- 10:30 PM GROMACS Bug #599: mdrun minimization crashes with GBSA / HCT and virtual site
Could you please provide me with your input .gro and .mdp - files, to speed the resolution of this bug.
- 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
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