[gmx-users] how salt concentration influence the cutoff distances for hbond and salt bridges
Smith, Micholas D.
smithmd at ornl.gov
Thu Aug 6 13:51:52 CEST 2015
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 Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of LW <wli148 at aucklanduni.ac.nz>
Sent: Wednesday, August 05, 2015 8:44 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] how salt concentration influence the cutoff distances for hbond and salt bridges
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.
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