Dear GMX Users I would like to let you know that I have run MD simulation on a Carbon nanotube- drug system.
All steps (Energy minimization, Postion restrained, Equilibration with NVT and NPT ensembles and finally MD) have been done successfully. Currently if would like to calculate binding free energy for the system (drug molecules inside Carbon nanotube). Here are my questions at this point; 1.May I know if I must add the free energy stuff to all the mdp files for each steps of (Energy minimization, Position restrained, Equilibration with NVT and NPT ensembles and finally MD) and redo all the simulation steps? I am wondering because I have seen few people who only edited the final MD.mdp file and add the free energy stuff. 2. I know to get the binding energy curve; I need to run several simulations, one for each lambda value. Hence, I need 21 point from Lambda=0 to 1 to get the smooth curve. To do this, I have to start with initial Lambda =0 as stated in the energy stuff below, in my mdp file. May I know which parameter(s) (init_lambda or foreign lambda or ...) need to be changed in my mdp file to do the next simulation and until the last simulation? I mean to go from Lambda=0.0 to the next lambda =0.05, 0.10, 0.15, … and 1.00. The free energy stuff in my mdp file is as below: ; Free energy control stuff free_energy = yes init_lambda = 0.00 delta_lambda = 0 foreign_lambda = 0.05 sc-alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 Your kind advice on this matter would be highly appreciated. Best regards Meisam
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