[gmx-users] How to implement dihedral restraints

Ryogo Sugitani rsugitani at ucdavis.edu
Tue Jan 23 20:44:21 CET 2007


I have a quick question on dihedral restraints.

What is the unit of dihre_fc in .mdp file?
(It's not on the User's manual)

> Add this to your .mdp
> ;dihedral restraints
> dihre               =  simple
> dihre_fc            =  100     ; or whatever value you desire
> dihre_tau           =  0.0
> nstdihreout         =  50

From the test I ran, it seems to be kJ/(mol deg^2 ),
but I would like to have confirmation from someone who knows it for sure
since I need to calculate exact restraint potential from dihedral angle
to calculate PMF profile along dihedral angle.

Thank you in advance,


On Wed, 13 Dec 2006 15:54:28 -0500, chris.neale at utoronto.ca wrote:
>> For example, my peptide is rotating 50 degrees about a bond B-C, out 
>> of four
>> bonded atoms A-B-C-D.  I want to apply additional force on this
>> dihedral(B-C) during my simulation(only for this particular atoms to 
>> make it
>> rotate further till 180 degrees). All the remaining atoms in the peptide
>> will have normal force as usual.
>> May I ask you, how can I apply this in gromacs code.
>> Any help will be appreciated!
> The current manual is good at describing what the options do for 
> dihedral restraints, but (to my knowlegde) doesn't explain at all how 
> to get the implementation up and running. Here is how I have done it 
> based on searching the mailing list for answers. I suggest that 
> something like this is added by way of example to the manual for 
> future releases.
> Also, the manual is a bit unclear about whether this type of dihedral 
> restraint is stable for use near 180deg. I have found that for my 
> system everything appears to behave normally and as expected over the 
> entire range of dihedral angles including 180deg.
> In your .top file:
> ; Include forcefield parameters
> #include "ffoplsaa.itp"
> ; Include topologies
> #include "myprotein.itp"
> [ dihedral_restraints ]
> ; ai   aj    ak    al  type  label  phi  dphi  kfac  power
>    A    B     C     D     1      1  180     0     1      2
> #include "tip4p.itp"
> etc...
> Make sure that the dihedral_restraints section comes immediately 
> after the inclusion of the protein topology. If you have the protein 
> topology directly in your .top file then just include 
> dihedral_restraints after the protein listing but before any mention 
> of things that are not that protein molecule.
> Add this to your .mdp
> ;dihedral restraints
> dihre               =  simple
> dihre_fc            =  100     ; or whatever value you desire
> dihre_tau           =  0.0
> nstdihreout         =  50
> For more information about what these options mean, please refer to 
> the manual.
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