[gmx-users] Distance constrained energy minimization and MD

[Mark Abraham]

jayant james wrote:
> Hi all!
> The protein that I am trying to simulate has 3 chains. My aim is to 
> apply harmonic constraints
> 
> to certain parts of the protein and (based on FRET derived distances) I 
> am attempting to incorporate distance constraint between certain amino 
> acids of different chains during EM and MD.

Constraints and restraints are different concepts in GROMACS. Look them 
up in the manual.

> _Harmonic Constraints_
> 
> I figured, that for the harmonic constraining the input is in the file 
> "posres_D.itp" and I specify
> 
> define = -DFLEXIBLE -DPOSRES in the em.mdp
> 
> _Distance constraints _
> 
> I would also like to have amino acids contrained, not by a fixed 
> distance but within a range(say 45-75 angstroms). How do I go about 
> doing this?

Check out distance restraints in the manual.

Mark