Is it necessary to set none for constraint algorithm in order to provide more flexibility for protein in MD simulation ( .mdp file) ?
in this case how long must be the ((dt)) parameter for each step , at top ?
Ricardo J Ferreira
Hi,
no. The constraint algorithm (LINCS) only works concerning bond lengths (to speed up calculations by fixing its length instead of treating them as harmonic bonds). The flexibility of the protein is given by the different bond, angle and dihedral combinations. Only if you apply position restrains (-DPOSRES keyword) you will have your protein fixed.
Usually, I keep the dt = 0.002
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