Mariana

Hello! I'm running a molecular dynamics of a protein, with periodic boundary conditions (my box of water), and the program NAMD. What I want to do is equilibrate my system first, by combining minimization and equilibration steps, so... in order to do that, when i take the last structure of my system, previously equilibrated at 1 atm and 300 K (with a value of "constrain" = 16 in backbone) and want to keep doing the equilibrium stage -now with a value of "constrain" = 14 to go gradually releasing restrictions in the backbone- and to not lose my protein secondary structure, from the beginning of the calculation it falls, warning that the simulation is unstable because the atoms have more speed than originally permitted. What do you recommend me in terms of the dynamic protocol to meet my goal? Thanks in advance, best regards from Venezuela.