In God We Trust Hello Dear Vaibhav Saraf > My system consists of the protein, water of crystallization and > additional water molecules. And before doing the position restraint > MD, I wish to perform energy minimization once with the protein and > its water of crystallisation fixed and only the additional water > molecules free. Later would do it un-restrained. > So need guidance on whether I can fix the protein (along with its > water of crystallisation) during energy minimization
you can make an index file and make a fix group consists of number of protein and water of crystallization and then in mdp file define freezegrps and freezedim ( Y Y Y ) and with MD integrator. Yours truly Karim Mahnam Institute of Biochemistry and Biophysics (IBB) Tehran University P.O.box 13145-1384 Tehran Iran http://www.ibb.ut.ac.ir/
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