Dear Tsjerk > Maxim, > > I'd guess that you're polylysine doesn't come charged without > having any > counterions in experiment. Indeed, but if we are using classical non-polarisable FF we already thrown off effects of protonation/deprotonation, charge transfer etc, do we? In the experiments, you're probably > dealing with > hydroxide ions (and an additional amount of hydronium ions). I'd > say these > will also influence the experimental findings. Therefore, there's > more sense > in adding counterions, maybe even positive and negative, This is exactly the point - when I added MORE ions - the system behaves better. It leads to a bit higher salt concentration than it is in experiment, but after all this discussion I realized that it is better way than constraining the ions.
> there is in > creating a weird unphysical system. > > Have you also considered that not all of your lysines need to be > protonatedat pH=7? You'd actually want a constant-pH simulation > with dynamic exchange > of proteins. But that's one bridge too far at present :) This is exactly what I want - but I guess I complete this project before I will have a chance to use it :-) Many thanks, Maxim > > Good luck, > > Tsjerk > > On 2/28/06, Mark Abraham <[EMAIL PROTECTED]> wrote: > > > _______________________________________________ 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
