[gmx-users] Applying Dihedral Restraints to Polymer in GROMACS 5.1

[Mark Abraham]

Hi,

It's a restraint - they move in the context of the force field and your
extra potential. They're not frozen.

Mark

On Tue, May 23, 2017 at 7:49 PM Harry Ponce <hponce61 at gmail.com> wrote:

> Hello,
>
> I'm attempting to run an energy minimization on some high energy conformers
> of a polymer dimer while restraining two dihedral angles pertaining to the
> five backbone carbons of interest. The literature and forums online are
> sparse when it comes to non-biochemical systems, and it seems as though the
> syntax might have changed over the updated versions of GROMACS.
>
> I've attempted to implement this bit in my topology:
>
> #ifdef DIHRE
>
> [ dihedral_restraints ]
> ; ai   aj    ak    al  type  label  phi  dphi  kfac  power
>     2    1     8    29     1      1  52      0     1      2
>     3    2     1     8     1      1  75      0     1      2
>
> #endif
>
> As well as this bit in my .mdp file:
>
> define            = -DDIHRE
> ; Dihedral Restraints
> dihre            = yes
> dihre_fc        = 1000
> dihre_tau        = 0.0
> nstdihreout        = 50
>
> I've also tried using what I think is the more recent syntax for applying
> restraints:
>
> ; position restraints for System of UNNAMED
>
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
>    2    1       1000       1000       1000
>    3    1       1000       1000       1000
>    8    1       1000       1000       1000
>   29    1       1000       1000       1000
>
> However, when I energy minimize and read the backbone dihedral angles they
> are different than the ones I started with! I am sure I have the correct
> atom numbers (1,2,3,8,29), but am not sure why GROMACS is reading them and
> then ignoring my restraints.
>
> Any ideas?
>
> Thank you very much,
> Harrison
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