GROMACS development

05/09/2019

06:01 PM GROMACS Task #2947: make an end to end test for membed

Is there a plan to introduce an integration test on membed once the bug is fixed?

04/16/2019

09:56 AM GROMACS Revision 102447a5: Die with helpful note in case of incorrect input to editconf with -conect

Previously editconf would give a cryptic error message
Assertion failed:
Condition: fio->xdr != nullptr
Implementatio...

04/15/2019

08:34 PM GROMACS Revision 9cc22661: fix formatting of editconf note

Change-Id: I628fc820a176fdc4b019e5819e6fa650842024d4

04/09/2019

05:49 PM GROMACS Bug #2922 (Rejected): mdrun confout puts box origin near zero

If I run editconf to move the location of the box with e.g. -translate or -rotate flags, the box will be correspondin...

11:29 AM GROMACS Bug #2920 (Rejected): grompp writes tpr value of nstcalcenergy different than mdp value

If you set nstcomm > nstcalcenergy, you will get a note that nstcomm is being set to nstcalcenergy. This will be refl...

04/07/2019

08:33 PM GROMACS Task #2723: Update mdrun-performance.rst to clearly express the nature of task

Sorry I will try to get to this soon. Helpful on this front was a conversation Christian and I had with the Scientifi...

01/20/2019

04:07 PM GROMACS Task #2727: Move non-analysis functions out of gmxana

Any script that currently uses make_ndx can trivially be updated by using the -on flag on select. There is a cost to ...

01/14/2019

11:10 AM GROMACS Task #2831: Bump required version numbers of infrastructure for 2020

From a user perspective, I don't think there will be much difference between CUDA 8 or 9. CUDA 9 supports GPUs going ...

01/12/2019

04:19 PM GROMACS Task #2829 (Rejected): mdrun appends when checkpoint specified by -cpi is not found

If I invoke mdrun with all paths correctly specified:
gmx mdrun -s md.part0001.tpr -cpi md.part0001.cpt -noappend
...

01/04/2019

06:00 PM GROMACS Task #2825: reportGpuUsage is misleading

I agree that there is not much value add to cleverly attempting to print back to stderr how mdrun was called. In gene...