Hi, I did the energy minimization of my protein (230 amino acids) after adding ions .. and after checking the potential energy of the system I was getting thee graph which is different from the one given in the lysozyme tutorial i.e. the the potential line in graph is not parallel to the x axix.. Here is are conditions that I used for minimization :
define = -DFLEX_SPC constraints = none integrator = steep nsteps = 50000 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no ------------------------ I got the following result :- Steepest Descents converged to Fmax < 2000 in 296 steps Potential Energy = -6.9540075e+05 Maximum force = 1.9863752e+03 on atom 1669 Norm of force = 3.7864201e+01 ------------------------------ I want to know which parameters are important to get a correct minimized structure and what value do I have to take for emtol and nsteps to minimize the structure properly.. Also how would I know that at what value of emtol my protein will be minimized.. I checked the manual to get some details but there only the basic theory of minimzation is written.. A detailed explanation will be more helpful... -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : [email protected]
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