What do you mean spurious protein movement? Also, the instantaneous electrostatic potential is always uneven, and I am not sure why the average electrostatic potential would change with excess salt, excepting that I would expect it to converge more rapidly with excess salt.
Finally, if you are going to end up showing this comparison, it would be best if you ran 2 independent simulations of each salt concentration. Without repeats I often find the conclusions in such comparisons hard to pin down to the change in the system as opposed to statistical variation. -- original message -- Thanks Chris, very good points. I would like to add a potential drawback for not using salt taken from my experience: I simulated a coiled coil with one end having charge +12 and the other zero. I ran a simulation with just 12 Cl- counter ions which tended to cluster near the positively charged tail. In that simulation the electrostatic potential in the box was uneven and that resulted to spurious protein movement at the positively charged end. I am now preparing a simulation with 0.15 M NaCl and zero net charge to see the effect on protein dynamics. But I haven't seen many papers using excess salt concentrations and that makes me worry about the validity of the results I will get. Thomas -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
