GROMACS development

09/26/2018

01:12 AM GROMACS Revision f7ba25f7: (Re-)fix typo in DD load balancing printing

Seems I42dcb3e5a8fa64f80cf480f4838a9f7fa70e03cd got lost in
Id3fcf6594b6f97129c72fe6f44c54d5c20afa11d. This patch res...

09/25/2018

08:35 AM GROMACS Revision 7687fffc: Remove obsolete braces in do_md()

In I17c9ae4c1c88bdb328e17e75fec55a558613cff0, we removed the rerun
functionality from do_md(), but left a pair of bra...

08:33 AM GROMACS Revision 11c0af7b: Remove rerun from do_md

As the rerun functionality is handled in a separate function now, this
commit removes rerun from do_md.
refs #1868
...

07:32 AM GROMACS Revision c52e6838: Remove unnecessary functionality from do_rerun

As discussed in task #1868, the rerun functionality gets reduced to essentially
"take a configuration and calculate f...

02:37 AM GROMACS Revision 8270c604: Prepare rerun commit

In Task #1868, we will break out rerun from the do_md code. This
results in new files, rerun.{h,cpp}, containing a do...

09/24/2018

01:32 AM GROMACS Bug #2649: Virial calculation necessary for correct energy calculation on GPU

Berk Hess wrote:
> I looks to me like the issue is on line 910 of sim_util.cpp:
> pmeFlags |= (flags & GMX_FORC...

06:29 AM GROMACS Bug #2649 (New): Virial calculation necessary for correct energy calculation on GPU

In the current implementation, the energy in do_md() is never calculated without the virial (see below for the respec...

09/21/2018

10:08 AM GROMACS Revision 564a67c0: Make CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS require global communication

Currently, giving the CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS flag, but
none of CGLO_TEMPERATURE, CGLO_STOPCM, CGLO_...

09/20/2018

12:33 AM GROMACS Bug #2647 (Blocked, need info): Removing CGLO_TEMPERATURE flag in MD Setup leads to fatal error because of missing bonded interactions

The first @compute_globals()@ call in the setup phase of @do_md()@ includes the flag for temperature calculation:
...

09/19/2018

11:43 PM GROMACS Bug #2417 (Accepted): Physical validation tests fail with default installation

This problem disappears when using a newer version of the physical validation package - change to be uploaded to gerr...