[gmx-users] Distance constrained energy minimization and MD

[jayant james]

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.

*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?
thanks
Jayant James

-- 
Jayasundar Jayant James

www.chick.com/reading/tracts/0096/0096_01.asp)
Residence -24935864, cell-9841042164
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