> Dear all, > > I am trying to simulate a ligand at the cavity of CB receptor with the > dmso environment. Even if I used very large number of steps for the > geometry optimization before simulation, I have some LINCS problem for the > solvent, I changed the solvent from dmso to water, but it didn't help the > solution.
http://wiki.gromacs.org/index.php/Errors#LINCS_warnings tells you a bit about this situation. There's some useful advice on alternatives for system preparation here http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation. In particular, you may wish to see if you can do EM and simulate in vacuo. Also starting your first MD run with position restraints is normally a good plan. > The input and output files are in below. They look OK to me. Mark _______________________________________________ gmx-users mailing list [email protected] http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
