Hello everybody I tried to work with gromacs employing free energy calculations in a dimeric protein system. First of all, doing a energy minimization a later to compute the binding energy. For all the cases, I use amber 94 FF. However, I have two questions.
1. When I made the energy minimization I got the following message: WARNING 1 [file topol_B.itp, line 10531]: Some parameters for bonded interaction involving perturbed atoms are specified explicitly in state A, but not B - copying A to B Although I could run that simulation. But, is this right to my simulation? 2. Is possible to use free energy methode (lambda, init_lambda, etc) to calculate only binding energy between the system told at the beginning?. I guess is possible typing zero for temperature. doesn't it? I appreciate your support! -- Jorge R. Quintero Químico Universidad Industrial de Santander Bucaramanga, Santander - Colombia -- 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
