[gmx-users] Distance constrained energy minimization and MD

jayant james jayant.james at gmail.com
Tue Mar 25 23:47:11 CET 2008

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?
Jayant James

Jayasundar Jayant James

Residence -24935864, cell-9841042164
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080325/c20627b8/attachment.html>

More information about the gromacs.org_gmx-users mailing list