[gmx-users] Ensemble averaged restraints
mesanthu at gmail.com
Fri Oct 14 20:08:39 CEST 2011
I have read in many papers where restraints have been applied to ensembles
of structures and I can theoritically think of that but I am not able to get
my head around on how to implement it.
Theoretically the method should do this :
1). Once we have N structures that we want to simulate in parallel we find
the ensemble averaged restraint potential and add it to the Forcefield
potential or compute the force on each atom based on this and add it to the
gradient of force-field.
2). Simulate each protein with this modified potential for some Nstep steps.
3). Collect all the conformations at the end of Nstep steps and then
recompute the restraint potential and redo from step 1 until convergence of
Since the restraint I am looking for is RDC's, I have to take extra care of
aligning all the snapshots once I collect them.
But how to actually implement it in Gromacs?? Should I write a script that
does this outside of Gromacs MDrun purview or is there an smart way of doing
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