[gmx-users] MDP define in GROMACS 2018

[Mark Abraham]

Hi,

On Mon, Jan 22, 2018 at 7:41 AM Joshua Mitchell <u5162401 at anu.edu.au> wrote:

> 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!
>

Sorry about that. The mdp handling is rather old and has quite a few
kludges in it, and it looks like we didn't test this case when we cleaned
up some aspects since the 2016 release branch. Thanks for the report.


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

We can probably do that for 2018.1. Meanwhile, I suggest you use something
like

define = -DPOSRE -DLARGEFC

...

#ifdef POSRE
#ifdef LARGEFC
#define POSREFC 1000.0
#else
#define POSREFC 500.0
#endif

...

because the issue is likely to be the '=' symbol in that .mdp field.


> 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, I'l look into that, too.

Mark


> Thanks,
> Josh
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