GROMACS development

06/12/2019

12:37 AM GROMACS Task #2976: Basic math for Multidimensional arrays

It's not clear to me whether these should be free functions or operator overloads.

12:37 AM GROMACS Task #2976 (New): Basic math for Multidimensional arrays

To use BasicMatrix3x3 as a drop in for the c-style tensor, we need to support the addition, subtraction, and several ...

06/02/2019

09:32 PM GROMACS Bug #2962: Segmentation fault, core dumped error

I looked into it, it looks like we're running out of memory. Your trr file box size is ~1000 nm, so I think something...

09:17 PM GROMACS Bug #2903: gmx wham doesn't compute profile with pull=angle-axis

Here's a simplified system, with a sample command run.

09:07 PM GROMACS Feature #1975 (Closed): grompp should warn if .mdp define does nothing

03/22/2019

06:32 PM GROMACS Bug #2903 (Closed): 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 ...