Hello everybody, I performed 100 simulation using a lambda step of 0.01 using gromacs 4.0.5 and Amber forcefield, starting always from the same structure ( a crystal with the ligand), minimizing for 3000 step and then starting the md simulation.
Here the row about the changing atom in my .itp file 15 amber99_48 1 M5P S15 1 -0.7162 32.0600 amber99_43 -0.7294 16.0000 and this is the mdp file concerning the free energy calculation: free_energy = yes sc_power = 1.0 sc_alpha = 0.5 sc_sigma = 0.3 delta_lambda = 0.0 init_lambda = 0.50 I succesfully wrote the topology for the alchemical transformation and in both end simulations ( with Lambda =0 and Lambda =1) I have no problem. For the intermediate steps( i.e. lambda=0.5) , however, I found that the Jennard-Jones and the Coulomb interactions are drammatically wrong. Actually, the S-O atom seems desappeared and the aminoacids in the active site change their position in order to reach a good equilibrium as if the S-O was not there ( there are charded atoms all around). Moreover the changing atom moves around going crushing against the other atoms sorrounding without apparent problems. How could it be? Can someone help me? Thank you! -- Ph.D. Student Matteo De Chiara Dept. of Molecular Biology, University of Siena Via Fiorentina 1, 53100 Siena Italy -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php