[gmx-users] Calculation for number of ions
jalemkul at vt.edu
Sun Aug 5 14:39:41 CEST 2018
On 8/5/18 6:35 AM, Archana Sonawani-Jagtap wrote:
> Hi all,
> I want to run simulation of GPCR in POPC bilayer, but the GPCR N-terminal
> is very flexible and negatively charged whereas the ICL's and C-terminal is
> highly positively charged. Thus, the they interact with each other during
> So, now I want to shield the negative charges of ICL's and C-term by adding
> ions near this region after neutralising the system. Is there any way to
> calculate the number of ions required for shielding.
> I tried physiological conc of 0.154 mole/L using genion command but it adds
> equal number of Na and CL ions.
You shouldn't simply add more ions of one type to your system. Doing so
will create a net charge that is then balanced by the PME neutralizing
plasma, but has been proven to induce artifacts, especially in membrane
genion has determined that your overall system is net-neutral, and as
such, adds an equal number of positive and negative charges to achieve
the concentration you request. If ions actually do interact in the
manner you believe, they will accumulate there over time during MD such
that the local concentration of Cl- ions is higher in a subset volume of
the system. There is nothing you should do to attempt to predispose the
system to this behavior.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
More information about the gromacs.org_gmx-users