Dear all, I am doing MD simulations of some polypeptide chains. These polypeptides have non-zero net charge; therefore, I should add some counterions into the box to use the PME. I am wondering – is there an elegant way to reduce influence of these counterions on polypeptide dynamics? Until now I see only two options for that: 1) Constrain ions somewhere far from the solute – but is doesn’t seem a good idea because the solute can move, and, therefore, contact the ions with time. 2) Make a “quasimolecule” - solute + ions and constrain the bond distances between solute and ions. Option 2) was proposed by Anton in some of his respond to the users of the mail-list. It looks better than opt. 1). But … I am a bit worrying about the difference between dynamics of such ‘quasimolecule’ and ‘natural’ dynamics of my polypeptide chain (a hypothetical case without ions). Could it help if I equal to zero the ion masses in opt 2)? Thank you all in advance.
With kindest regards, Maxim. Maxim V. Fedorov Research Associate. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
