Hi all,
I am using Gromacs version 4.5.6 for peptide simulation. The
structure of the peptide (16mer) was predicted from Pepfold3 server. I did
Simulated annealing so that the side chains get properly oriented and the
predicted structure will reach its global optimum so that the structure
becomes more stable for production run. I have doubt in the mdp paramteres
regarding position restraints and the annealing time and temperature. I
tried with position restraints so that the backbone is restrained and the
side chains are free to move. The annealing was pretty good. I did SA after
NVT. I dont know to proceed further. How to finalize the mdp parameters
like pressure couping and generate velocities for simulated annealing?
Thanks in advance.
K.L. Venkatraman
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