Dear George,thanks for the references. In any case, it is probably useful to check how the ion distribution is changing over time and maybe discard the initial part where it has not yet reached some sort of equilibrium. As for the size of the box, I will first see if recalculation of experimental data, translational diffusion coefficients from NMR, is affected.Kris
On Saturday, July 7, 2018, 6:35:08 AM GMT+2, George M. Giambasu <giambasu.gmail.com> wrote:
Here are few further points to consider when trying to reach a desired
salt concentration in nucleic acids MD simulations:
- the resulting salt concentration after equilibration will be different
from any initial guess, and so, in order to reach a desired
concentration you will want to iteratively change the composition of
your system and equilibrate (here is an example:
http://dx.doi.org/10.1021/jp306598y).
- equilibration of ions and water takes a long time: tens of nanoseconds
for simple helical nucleic acids and at least one order of magnitude
more for cases where ions might bind in cavities.
http://www.pnas.org/content/101/41/14771 is a good starting point.
- imposing specific solution salt conditions refers to maintaining a
specific *bulk* salt concentration, that is the ion concentration in
regions remote from the nucleic acid solute where the local density of
ions is not perturbed by the presence of the nucleic acid.
- typical simulation boxes (having clearances of 10-15 Ang.) are not
able to model a solution bulk, as one has to go *at least* 25 Angstroms
away from the nucleic acid surface to reach the bulk. So, if you want
your your simulation to reflect specific salt conditions (that can be
replicated experimentally) you better choose a large enough box (see
more here: https://doi.org/10.1016/j.bpj.2014.01.021 ,
https://doi.org/10.1016/j.jmb.2009.05.071).
best,
George
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. George M. Giambasu, Ph.D.
Rutgers, The State University of New Jersey
174 Frelinghuysen Road, Room 308E Piscataway,
NJ 08854, USA
giambasu.rutgers.edu
giambasu.gmail.com
rci.rutgers.edu/~giambasu
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Received on Thu Jul 12 2018 - 12:30:02 PDT
