Previous Thread
Next Thread
Print Thread
Counter-ions and PME
#38303 07/19/21 08:37 PM
Joined: Sep 2018
Posts: 10
C
ca4930 Offline OP
Forum Member
OP Offline
Forum Member
C
Joined: Sep 2018
Posts: 10
I'm trying to determine the impact of charge on an aspartic acid in my protein. I've setup a simulation in which the aspartic acid is neutral and one in which it's negatively charged. My conundrum is that if I use PME I must have counter-ions to accurately compute long-range electrostatics - however, neutralizing both systems would ultimately negate my exploration of charge. I've always run simulations with PME and I'm wondering if not including it in this case would be appropriate. Is there a work around that I'm missing?

Last edited by ca4930; 07/19/21 09:12 PM.
Re: Counter-ions and PME
ca4930 #38304 07/19/21 09:52 PM
Joined: Sep 2003
Posts: 8,582
Likes: 11
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,582
Likes: 11
PME is most reliable for a system that has no net charge, but there are provisions for cases where that is not the case, esp. for free energy simulations where the charge changes over the course of the simulation. However, I'm not certain exactly how it's done; it involves the QCOR keyword, and the default value is 0.0 for neutral systems, but it is not clear to me what to use for other cases.

BTW, the Ewald docs appear to incorrectly state the default for QCOR is 1.0; the source code now sets it to 0.0, since a solvated system is the usual case.

Last edited by rmv; 07/19/21 09:58 PM.

Rick Venable
computational chemist

Re: Counter-ions and PME
rmv #38305 07/20/21 05:37 PM
Joined: Sep 2018
Posts: 10
C
ca4930 Offline OP
Forum Member
OP Offline
Forum Member
C
Joined: Sep 2018
Posts: 10
Thanks for your reply. Yes, free energy methods seem to be more nuanced - but here, I'm not sure that I should mess with the QCOR parameter as I have a solvated, periodic system. In thinking about it more, it isn't clear to me that neutralization with counterions (hence allowing the use of PME) would necessarily impact the micro-environment of the protein where the charge change is taking place? I'm trying to avoid constant pH simulations....

Last edited by ca4930; 07/20/21 05:46 PM.
Re: Counter-ions and PME
ca4930 #38306 07/20/21 06:00 PM
Joined: Sep 2003
Posts: 8,582
Likes: 11
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,582
Likes: 11
Peptides and proteins can have a range of net charge values, so adding counterions to achieve a net zero charge for the entire system is fairly standard practice. I generally add ca. 100 mM excess salt, so that outcome is less sensitive to initial ion placement. I agree about avoiding constant pH methods.


Rick Venable
computational chemist


Moderated by  lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 7.3.31-1~deb10u1 Page Time: 0.009s Queries: 22 (0.005s) Memory: 0.7316 MB (Peak: 0.7767 MB) Data Comp: Off Server Time: 2021-12-08 00:20:01 UTC
Valid HTML 5 and Valid CSS