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 On 11 October 2012 20:22, Christopher Neale <chris.ne...@mail.utoronto.ca>wrote: > There are 4 reasons that I can think of: > > A) Didn't consider it or know how to do it > B) Repeating a previous simulation (possibly with some modifications) -- > e.g. simulation a protein in a lipid bilayer > using lipid parameters that have been shown to give the desired area per > lipid in the absence of salt but which > have not been evaluated in the presence of salt. > C) No parameters for desired salts, such as the common phosphate buffered > saline, in some force fields. > D) Trying to avoid unexpected and sometimes difficult to understand > effects of salt binding to the protein, salt > entry into a channel, etc. This is probably misguided because such things > are possible once you have even a single > counter-ion, but it is the reason that I have avoided the use of excess > salt in the past. However, in my more recent > work I have started adding excess salt around the concentrations that you > mention. > > I'm sure that there are lots of other reasons. > > Chris. > > -- original message -- > > Dear GROMACS users, > > In most of the papers that compare the results from MD with NMR data the > authors use just counter ions to neutralize the system. However, a salt > concentration of 0.10-0.15 M would be closer to the buffer solution used in > the NMR experiment. Why then people don't use more salt in their > simulations? Do they want to avoid ff inaccuracies or to be able to use a > shorter cutoff for the short range interactions? I would be very interested > to know the reason. > > thanks, > 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 > -- ====================================================================== Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- 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
