[gmx-users] adding constraints

Samuel Flores samuel.flores at yale.edu
Sat Dec 18 03:42:25 CET 2004


I'm new to gromacs and having trouble adding constraints.  I'm working 
with the included demo file and trying to add constraints.  I added 
"define = -DPOSRES" to the parameter file md.mdp, expecting all the 
protein heavy atoms to become constrained, but it didn't happen-- the 
protein kept moving in an unconstrained fashion..  Upon further 
investigation I found that even in the equilibration run, which produces 
cpeptide_pr.trr, the protein was not constrained, but was moving in 
contradiction of the demo documentation! 

Can someone tell me what's going on, and how i should go about 
constraining some of the DOF's??

Many thanks,


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