[gmx-users] about salt concentration
chris.neale at mail.utoronto.ca
Thu Oct 11 19:22:37 CEST 2012
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.
-- 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.
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