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
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