[gmx-users] simulation with position constraint by a harmonic potential

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 26 23:26:31 CEST 2011

Liu, Liang wrote:
> I am running Gromacs for RNAs, and I got a problem during the simulation:
> How to perform the simulation with each heavy atom constrained to its 
> initial position by a harmonic potential, E = k(r-r0)^2?

What you want are position restraints, not constraints (which are for bonds). 
pdb2gmx should have generated a posre.itp file for this purpose.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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