Hi all I have a question on umbrella sampling results under varied ionic strength. I have just done some regular umbrella sampling on the system of glucose 6-phosphate (small ligand molecule) on oligopeptide with LYS side chains. I mostly follow the tutorial by Justin <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bevanlab.biochem.vt.edu_Pages_Personal_justin_gmx-2Dtutorials_umbrella_index.html&d=DwIFaQ&c=nE__W8dFE-shTxStwXtp0A&r=gCy395jfSTIKIGBjdJ8SwSg8yN7wywRqF0ilx8ZoefpMNPZKIUY0jXzHKcFUwcQV&m=wjjoIomb4xozoyp9lqY4_wEzyhxGWILHcyUjAvXhess&s=--TZVWbKNWMqlgnHsfsMQUCzOJsx1PMTs4thX-y0jhM&e= >. I use explicit ions to represent the ionic strength level.
There is hardly any difference between my calculated adsorption energy (by PMF) under different ionic strengths (0, 20, 40, 70, 120 mM). However, we did observe apparent difference on surface retention time in regular MD simulations, which indicated a weaker surface interaction. During my simulation, the sampling time is 10 ns for each window, and I am wondering if the effect of explicit ions need longer simulation time to be reflected on results. Here is some detail of my simulation: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.evernote.com_l_AAMCVXRkp3tPYrhq-5F4oRHdtfnRb1VJo71U0_&d=DwIFaQ&c=nE__W8dFE-shTxStwXtp0A&r=gCy395jfSTIKIGBjdJ8SwSg8yN7wywRqF0ilx8ZoefpMNPZKIUY0jXzHKcFUwcQV&m=wjjoIomb4xozoyp9lqY4_wEzyhxGWILHcyUjAvXhess&s=B67nP5cwU6r5g_KBORUyrzAardEsfEzcojVKVZFomfU&e= I will appreciate it if anybody with relevant experience can give me some suggestion on this. Thank you. Yuanchao Liu (εε θΆ ) Ph.D. Candidate Department of Chemical Engineering and Materials Science 428 South Shaw Lane, Room 3263 Michigan State University East Lansing, Michigan 48824-4437 Email: ycliu1...@gmail.com; liuyu...@msu.edu; liuyu...@egr.msu.edu Cell:+1 (517)-763-1806 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
