[gmx-users] How to use "define = -DPOSRES" in Gromacs 2018?

[Kevin Boyd]

To add to Mark's comments, it's commonly the case that you want to apply
restraints based on the starting configuration, e.g. for restraining
protein positions at the beginning of a run. As the warning message says,
you can pass the same file to both -c and -r for these cases.

Also, you're correct that a version mismatch is why the tutorial doesn't
cover this issue - the -r flag is mandatory as of Gromacs 2018 if you're
using restraints. A more up to date set of tutorials for a number of
simulation setups (currently Gromacs 2018) can be found here:
http://www.mdtutorials.com/gmx/

On Mon, Jan 14, 2019 at 9:31 AM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> The purpose of applying position restraints is to restrain the coordinates
> to a set of target coordinates. grompp now requires you to be explicit
> about what target you choose. You need to decide what they are, and pass
> the file containing them to grompp -r.
>
> Mark
>
> On Mon, Jan 14, 2019 at 3:17 PM ZHANG Cheng <272699575 at qq.com> wrote:
>
> > Thank you Mark!
> >
> >
> > Sorry, I do not have a "targetcoords.gro" for the grompp.
> >
> >
> > I was trying to use
> > "gmx grompp -p system.top -c solvated.gro -f minimization.mdp -o
> > minimization.tpr",
> > and the "system.top" has a line of " #include "Protein_A.itp" ",
> > and the "Protein_A.itp" file has the restraints I need.
> >
> >
> > Should I modify the "minimization.mdp" instead?
> >
> >
> > ------------------ Original ------------------
> > From:  "ZHANG Cheng"<272699575 at qq.com>;
> > Date:  Mon, Jan 14, 2019 09:53 PM
> > To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
> >
> > Subject:  How to use "define = -DPOSRES" in Gromacs 2018?
> >
> >
> >
> > My backbone restraints is shown in the "Protein_A.itp" file:
> >
> >
> >
> > #ifdef POSRES
> > #ifndef POSRES_FC
> > #define POSRES_FC 1000.00
> > #endif
> >  [ position_restraints ]
> >       1    1    POSRES_FC    POSRES_FC    POSRES_FC
> >       3    1    POSRES_FC    POSRES_FC    POSRES_FC
> >       5    1    POSRES_FC    POSRES_FC    POSRES_FC
> > ......
> >     162    1    POSRES_FC    POSRES_FC    POSRES_FC
> >     163    1    POSRES_FC    POSRES_FC    POSRES_FC
> > #endif
> >
> >
> >
> >
> > The Martini protein tutorial said: specify "define = -DPOSRES" in the mdp
> > file for "gmx grompp".
> >
> >
> > However, adding "define = -DPOSRES" to the mdp file causes the error:
> >
> >
> >
> >
> > Fatal error:
> > Cannot find position restraint file restraint.gro (option -r).
> > From GROMACS-2018, you need to specify the position restraint coordinate
> > files
> > explicitly to avoid mistakes, although you can still use the same file as
> > you
> > specify for the -c option.
> >
> >
> >
> >
> > The tutorial uses Gromacs 5, but I am using Gromacs 2018. Is this the
> > problem for that?
> >
> >
> > How can I trigger those restraints in "Protein_A.itp" file using Gromacs
> > 2018?
> > --
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