[gmx-users] question about dihedral constraints

[Justin Lemkul]

On 1/10/13 9:28 PM, Tom wrote:
> Dear Gromacs Users,
>
> I want to use dihedral constraint in gmx.
>

First, you should understand that constraints and restraints refer to very 
different ideas:

http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints

> I directly type the following onto my  topol.top file :
> --------------------------------------
> [ dihedral_restraints ]
> ; ai   aj    ak    al  type  label  phi  dphi  kfac  power
> ; phi C'(n-1) - N - CA - C'
>     506    505     502    503     1      1  180     0     1      2
> --------------------------------------
>
> Do I also need to add these to *mdp file?
> ---------------------------------------
> dihre                     = yes
> dihre_fc                  = 15000
> -------------------------------------

Everything you need to know is either in the manual or on the website:

http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints

> Because I only need to contraint some of the dihedrals,
> I will  not constraints all of them.
> If I add the above on  *mdp file, will all the dihedrals be constrainted?
>

A simple test should be very illuminating.  You will get a dihedral restraint 
energy written to the .log and .edr files, and either your dihedral will be 
restrained or not (easily measured by g_angle).

> Another quesiton is what is the format of this dihedral constraints
> on *rtp file? How about the angle constraints? That would save a lot
> of work if pdb2gmx can automatically add these constraints to *top file.
>

That's what genrestr is for.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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