Well, you made a point of "Ions are big issue in MD simulations". Could you please hint me what possible issues, so I can search relavent to those keywords.
The main issue is the charge transfert which is not possible to model with a basic MM force fields. Then simulating a protein with an ions becomes an issue ! One reasonable think to do is to define convalent bonds between the ions and the atoms interacting with it in the protein. You won't see any change in the ion coordination ... that should apply to your system. Look the email list this issue was discussed many times. XAvier _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
