[gmx-users] Question on Umbrella Sampling with varied ionic strength.

[Yuanchao Liu (MSU)]

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=NpiNrs4JMs7x7VUghg3wpVUJ_O9DzzTJ8Mf9sATZN4E&m=BARutmaSsjnyhUuJ1NkYpSuBLCDEspqRUVRAXBYSUjQ&s=9L52pxEuFcjHHeCYHv5KvrMyWeV3meWk9qJVA1CenQo&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=NpiNrs4JMs7x7VUghg3wpVUJ_O9DzzTJ8Mf9sATZN4E&m=BARutmaSsjnyhUuJ1NkYpSuBLCDEspqRUVRAXBYSUjQ&s=KihiO_75Ay2xIRdGttNqM_4P72Pq4rWLizplUq9mr3Q&e= 

I will appreciate it if anybody with relevant experience can give me some
suggestion on this. Thank you.


Yuanchao Liu (刘元超)
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: ycLiu1987 at gmail.com; liuyuan6 at msu.edu; liuyuan6 at egr.msu.edu
Cell:+1 (517)-763-1806