Re: [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  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   ajakal  type  label  phi  dphi  kfac  power
> 21 829 1  1  52  0 1  2
> 32 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   fcxfcyfcz
>11   1000   1000   1000
>21   1000   1000   1000
>31   1000   1000   1000
>81   1000   1000   1000
>   291   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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[gmx-users] Applying Dihedral Restraints to Polymer in GROMACS 5.1

[Harry Ponce]

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   ajakal  type  label  phi  dphi  kfac  power
21 829 1  1  52  0 1  2
32 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   fcxfcyfcz
   11   1000   1000   1000
   21   1000   1000   1000
   31   1000   1000   1000
   81   1000   1000   1000
  291   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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