Dear Gmx users,
I would like to perform MD simulations of Membrane protein systems with high salt concentration. Initial structures were prepared using Charmm-gui. I would like to use 2 M KCl for these systems. I have some questions.
- Is it possible to use this kind of high concentration?
- Do you have suggestion of some references for possible effects?
- How does gmx genion estimate the number of ions? (If possible Charmm-gui also, sorry for that I know it is gromacs forum.)
CHARMM NaCl and KCl parameters have been validated via osmotic pressure up to 5 M: http://dx.doi.org/10.1021/jz900079w
genion uses the total box volume to compute the number of ions, CHARMM-GUI computes the actual solvent volume (excluding membranes, proteins, etc) to compute this quantity. The latter is more accurate; at low concentration the difference is probably negligible but at higher concentrations, the discrepancy could be quite large.
Dear Dr. Justin,
Thank you very much for your kind reply. It is very helpful.