From: Fateme Ghadirian (fateme.ghadirian_at_yahoo.com)
Date: Tue May 15 2018 - 03:28:02 CDT
Thanks for replying to my question. I've turned off warpAll and it did work.I will study the articles which you've recommended. But as a question:Are you saying that this way of constraining the ions can cause artificial or unphysical effects in my system or just that it's not a conventional way?
On Monday, May 14, 2018, 8:30:24 PM GMT+4:30, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov> wrote:
Turn off wrapAll. NAMD is wrapping the coordinates before tclBC sees them, and as a result they aren't actually being restricted from switching sides, at least based on the small force constant you used. However, if you are using PBC, it isn't really correct to think about an "upper" and "lower" side of your membrane, since the aqueous compartment is naturally connected across the periodic cell. The conventional way of handling this if you want different ion concentrations in two compartments is to make a system with two bilayers, and fill only one of the two systems with ions. Others have made approximately semi-periodic concentrations by applying external forces to the ions (10.1085/jgp.201311014), some of whom frequent this list and may be able to provide the NAMD inputs they used.
On 2018-05-14 08:18:20-06:00 owner-namd-l_at_ks.uiuc.edu wrote:
Dear NAMD users,
I have a POPE bilayer which is solvated in water and some ions just on the upper side of my membrane. During the run, due to the periodic boundary condition, some of them go from the upper boundary and come from lower boundary, so I have some unwanted ions in the inner side of my box.As a solution for this problem, I’ve used tclBC to apply a hard wall in Z direction, and added it to my conf file, then performed the simulation, but it did not work! So I still have unwanted ions in lower side of the box. The conf and tclBC files are incorporated to this email. (TclBC code is written in a general case which there are ions in both sides of the membrane and also prevents PBC for ions in Z direction, clearly this is not the reason of the failure.)Is there anyone who knows why this is not working?
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