GROMACS development

03/22/2019

06:32 PM GROMACS Bug #2903 (Feedback wanted): gmx wham doesn't compute profile with pull=angle-axis

Given correct tprs and pull files on a set of umbrella windows maintained using angle-axis, the histogram is computed...

03/19/2019

02:58 PM GROMACS Task #2898: Naming common variables

One suggestion - I'd naively interpret computeVirial and compte_dHdLambda as a verb, so that seems to me more like a ...

02/09/2019

05:59 PM GROMACS Revision 20e2a461: Use more vector in selection index groups structs

Removed unused functions
Change-Id: If8a90ef705c3a9c9ab641ddbb64d17607d7a610f

02/07/2019

12:35 AM GROMACS Feature #2860: Option for outputting min/max coordinates in gmx traj

Hi,
For the functionality you describe, it's pretty easy to just e.g. calculate the z coordinate of the protein of...

02/04/2019

07:47 PM GROMACS Feature #868: Implement parallelization support to analysis framework

Kevin Boyd wrote:
> OK in that case it's probably easier to go with your first suggestion. So for each thread, I'll ...

07:36 PM GROMACS Feature #868: Implement parallelization support to analysis framework

OK in that case it's probably easier to go with your first suggestion. So for each thread, I'll have to manually set ...

06:22 PM GROMACS Feature #868: Implement parallelization support to analysis framework

Teemu Murtola wrote:
> The selection code is indeed not thread safe (and cannot be made such, without a lot of work ...

02/02/2019

07:39 PM GROMACS Feature #868: Implement parallelization support to analysis framework

Teemu Murtola wrote:
> The selection code is indeed not thread safe (and cannot be made such, without a lot of work ...

06:05 PM GROMACS Feature #868 (In Progress): Implement parallelization support to analysis framework

I have WIP for simple std::thread based parallelism over frames, based on the doxygen flowchart that Teemu put togeth...

01/21/2019

11:42 AM GROMACS Revision 70bacbcf: Convert gmx_update_t to C++

gmx_update_t replaced with Update class with pImpled
implementation class
Fixes an end of mdrun leak
Put Update on ...