(no subject)

From: jeevan gc (gcjeevanbdr_at_gmail.com)
Date: Thu Jan 24 2019 - 16:53:46 CST

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

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