RE:

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Jan 25 2019 - 11:59:35 CST

If you want to disallow lateral protein motion completely, why not just use constraints? http://www.ks.uiuc.edu/Research/namd/2.13/ug/node27.html#SECTION00086200000000000000 Just tag the protein and use selectConstraints to only use lateral constraints. However, in practice you really shouldn't care if your membrane drifts, and my usual practice has been to ignore it unless I need to make an animation. Proteins and membranes move, and that's just a fact of life. I'd recommend turning off wrapAll, and then just rewrapping afterward in VMD, possibly even recentering the protein prior to rewrapping.

-Josh

On 2019-01-24 16:00:34-07:00 owner-namd-l_at_ks.uiuc.edu wrote:

Dear all,
We have come across an issue on protein and membrane regular MD simulations. We are also aware of the fact that this issue is just about visualization and should be taken care by the Periodic Boundary Conditions. The membrane size is sufficient enough to avoid any overlap in periodic image as the protein drift from the edge of the membrane. The wrap all is also turned on. The namd mailing list provided us important information and suggestions about this issue but still not able to completely solve this issue.
Below are list of simulations we would like to practice to avoid the drift of the protein from the membrane edge.
1. Increased the step6.6 equlibration simulation step obtained from CHARMM-GUI to 10ns or higher.
2. Increase the damping constant from 1 to 2 ps.
3. Increased the size of the membrane.
4. Applied the minimal restraint to the protein and the membrane system.
5. NPT/NVT minimization
We tried Simulation #1, it didn't help. The protein drifted from the edge of the membrane. Is it necessary to increase damping coefficient to 2ps as suggested by James Starlight?
If these only visualization issues, increasing the size of the membrane will increase the simulation time and we don't benefit much.
Simulation #4, restraining either protein of membrane COM may create an artifact in protein membrane interactions.
As CHARMM-GUI minimization steps suggested, we performed step6.1 and step6.2 in NVT, step6.3 to step6.6 in NPT ensemble. Production run was performed on NPT.
Are there any best practices to avoid such drift of protein in the membrane? Any advice will be greatly appreciated.

Thank you in advance.
Jeevan

--
Jeevan B. GC, Ph.D
Post Doctoral Research Associate
Department of Pharmaceutical Sciences
Washington State University
Spokane, WA 99224 , USA

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