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

[Mark Abraham]

Hi,

On Mon, Jan 14, 2019 at 2:54 PM ZHANG Cheng <272699575 at qq.com> wrote:

> 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.
>

We've tried to get you to think, and then do

gmx grompp -r targetcoords.gro -c initialcoords.gro

for the files that make sense. Please help us make that clearer!

Mark


>
> 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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