Hello users I am using the gromacs 3.3 with 43a1 force field. I am using a restraint force of 50 intially during the beginning of protein simulation in water, even after such a high value of restraint force i can see some major deviations in my structure during the simulation.
My doubt is that since i am applying enough restrain force on the protein it should not deviate at all from its native conformation. I want to know is this the usual behavior in gromacs or i am making some mistake in applying restrain. I am using a posre.itp file using define = -dposre in the .mdp file for applying the restraining force. With regards Gurpreet
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