Applying pressure on membrane protein system

From: Sruthi Sundaresan (bo20resch11002_at_iith.ac.in)
Date: Thu May 12 2022 - 00:08:42 CDT

Dear Users,
I would like to know how to apply pressure on a membrane protein in one
direction. I am running the simulations on NAMD3.0 and used the following
lines in the input files to apply pressure:

*useConstantArea yes;*

*SurfaceTensionTarget 0.0;*

*langevinPiston on;*

*langevinPistonTarget 4000.00;*

*langevinPistonPeriod 100.0;*

*langevinPistonDecay 50.0;*

The above lines help to apply pressure on the z-axis alone while keeping
the area of the x-y plane constant.
However, I'd like to know how to apply pressure selectively in one
direction alone (either +z or -z) and if there's any way by which I can
apply pressure to a certain predefined plane alone or set of atoms.

Thanks and regards,

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Sruthi Sundaresan

Ph.D. Research Scholar

C/o Dr. Thenmalarchelvi Rathinavelan

Molecular Biophysics Lab, Department of Biotechnology

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