GROMACS development

10/19/2018

11:32 PM GROMACS Feature #1168: g_density does not do what users think it does, given PBC over z and constant pressure simulation

This bug still exists up (tested in version 2018.3). The effect will be subtle for realistic bilayer fluctuations. I ...

11/07/2017

05:35 PM GROMACS Feature #2288 (Accepted): gmx msd doesn't optimally handle missing input trajectory frames

I am reporting an issue with the gmx msd command from gromacs version 5.1.2. The issue is that when the input .xtc fi...

06/08/2017

06:23 PM GROMACS Task #2202 (Closed): stop using cute abbreviations in help files

For example, gmx traj has the text "-[no]mol Index contains molecule numbers iso atom numbers" where I guess iso mean...

05/31/2017

03:43 PM GROMACS Feature #2194: xvg output requested as an output option in place of xpm files

Not to disregard other formats, but the .xvg output if e.g. gmx pairdist can have an enormous number of columns for c...

05/30/2017

11:00 PM GROMACS Feature #2194 (Accepted): xvg output requested as an output option in place of xpm files

Some analysis tools have output options that would be useful as .xvg files with real numbers but are only provided as...

05/11/2017

07:42 PM GROMACS Bug #2171: editconf -h indicates -center defaults to (0,0,0) but that is not true from a user perspective

Looks good. Thanks Justin.

07:14 PM GROMACS Bug #2171: editconf -h indicates -center defaults to (0,0,0) but that is not true from a user perspective

Thank you Justin. However, it is unclear to me how this code change solves the issue. I think a better text output wo...

05/07/2017

11:00 AM GROMACS Bug #2171: editconf -h indicates -center defaults to (0,0,0) but that is not true from a user perspective

Not sure what "feedback wanted" means. Is it feeback from me? In that case I did try to follow the gerit link but I c...

05/06/2017

01:42 AM GROMACS Bug #2171: editconf -h indicates -center defaults to (0,0,0) but that is not true from a user perspective

OK, but I think we're still talking about different things. I don't care that -center failes without an argument. Wha...

08:19 PM GROMACS Bug #2171: editconf -h indicates -center defaults to (0,0,0) but that is not true from a user perspective

Agreed changing it to -999's is a terrible idea. That was my (clearly bad) way of trying to clarify my point. If peop...