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
--
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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