[gmx-users] about salt concentration
chris.neale at mail.utoronto.ca
Thu Oct 11 23:01:51 CEST 2012
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.
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