Levi, If you are comparing between the two concentrations, your cutoffs (i.e. the defined measures) should not be changed. If you are trying to determine if you can re-construct the averages from the bulk solution from the 200mM NaCl solution than you will need to sweep through a variety of cutoffs and see which one matches best; though will increasing salt, you can imagine that the electrostatics that lead to the formation of salt-bridges will be screened (weakend) and you may find less of them.
-Micholas =================== Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics ________________________________________ From: [email protected] <[email protected]> on behalf of LW <[email protected]> Sent: Wednesday, August 05, 2015 8:44 PM To: [email protected] Subject: [gmx-users] how salt concentration influence the cutoff distances for hbond and salt bridges Dear all, I ran two simulations of my protein, one in the absence of NaCl, and another in the presence of 200 mM NaCl. With the simulated trajectories, I am not certain how salt concentration influence the cutoff distances for hbond and salt bridges. Any help is grately appreciated. Best regards, Levi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
