From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Fri Apr 30 2021 - 08:59:01 CDT
What did you do to your periodic box size in the NAMD configuration file, and how is the barostat allowed to change it? Normally, the x-y dimensions are the same between the two membranes, so you use the semi-isotropic ensemble options for the barostat (useflexiblecell yes, useconstantratio yes), and it is quickly impossible for water to cross either membrane without going through it. If you are getting water channels in your membrane, the x-y dimenstions may have been too large in the beginning, and the fast water diffusion formed a stable pore.
On 4/30/21, 5:03 AM, "owner-namd-l_at_ks.uiuc.edu on behalf of José Villalaín" <owner-namd-l_at_ks.uiuc.edu on behalf of jvillalain_at_umh.es> wrote:
I am trying to build a system with two membranes in order to place
different concentrations of ions (inside/outside). To do this, I have
minimized, equilibrated and simulated a single membrane system
(containing membrane, protein, ions and water).
To obtain the system with two membranes, I use the previous system
containing one membrane, duplicate it and join the two systems in one.
Afterwards, I remove all the water and ions, solvate with water, remove
the water inside the membrane and place the ions (different
concentrations inside and outside).
However, and although I have used several different parameters in the
configuration file (different constraints for water, lipids, ions and
their combinations, PME, not PME, pressure on /off), whenever I try to
equilibrate the system, it shrinks, specially the water molecules, and
the water and ions move to the sides and from the sides, move from/to
the different compartments .
So far it has been impossible for me to continue equilibrating the two
Could someone give me an idea of what I am doing wrong?.
Thank you very much in advance.
IDiBE / UMH
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