Restraints allow, by definition, for slight deviations.
Erik
On Mar 14, 2013, at 12:51 PM, Shima Arasteh wrote:
Dear gmx users,
I want to use restraints on backbone of my protein to keep its
secondary structure during minimization and equilibration steps. To
do so, I generated backbone-restrain.itp and then included it to top
file. Next, added define = -DPOSRES to minim.mdp file.
After minimization, when I check the minimization output file, I saw
that the backbone of input and output files are not exactly the same.
Is there any step which I have not done to set the restraints
correctly?
Thanks in advance.
Sincerely,
Shima
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