[gmx-users] MDP define in GROMACS 2018

[Joshua Mitchell]

Hi all,

I am excited to try out the new PME code in GROMACS 2018! It seems that
preprocessor variables can no longer be given values in the MDP as of
GROMACS 2018? So in 2016 I could do

define = -DPOSRES -DPOSRESFC=500.0

and then in the posres ITP:

#ifndef POSRESFC
#define POSRESFC 1000.0
#endif

[ position_restraints ]
; atom  type      fx      fy      fz
    1     1  POSRESFC  POSRESFC  POSRESFC
    4     1  POSRESFC  POSRESFC  POSRESFC
    7     1  POSRESFC  POSRESFC  POSRESFC
....

And this would let me set the position restraint force constants from the
MDP, which was very convenient. I'm pretty sure I got this trick from
MARTINI so I'm not the only person who uses it. Frustratingly, in 2018 that
little equal sign causes the whole MDP define line to be ignored, causing
position restraints to fail silently. So I've spent all day trying to
figure out why it looked like my position restraints aren't working!

I think this could trick a lot of people, especially newer users trying out
MARTINI. Is the old behaviour coming back?

Oh and also, the link at http://manual.gromacs.org/documentation/ to the
2018 release notes goes to the RC-1 release notes, not the full version
release notes - seems to be missing a hyphen in the URI.

Thanks,
Josh