[gmx-users] MDP define in GROMACS 2018
mark.j.abraham at gmail.com
Tue Jan 23 11:23:51 CET 2018
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
> [ 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
define = -DPOSRE -DLARGEFC
#define POSREFC 1000.0
#define POSREFC 500.0
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.
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