Re: Applying pressure on membrane protein system

From: Geist, Norman (
Date: Thu May 12 2022 - 00:26:04 CDT


the input looks fine for applying the pressure in only one direction
(Z), however, you might need to set "useflexiblecell yes", too. Away
from that, there's no different on the direction of applying the
pressure (-z or +z) as it is same thing (periodic boundary condition).
Do you mean compressing or strechtich the box? In this case, the sign
of the applied target pressure will probably give you the direction.

Unfortunately, you can't select atoms to apply the pressure on. In
this case, you may be more interested in constant velocity or constant
force pulling.

Norman Geist

Am Donnerstag, den 12-05-2022 um 07:08 schrieb Sruthi Sundaresan:

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

Thanks and regards,


Sruthi Sundaresan

Ph.D. Research Scholar

C/o Dr. Thenmalarchelvi Rathinavelan

Molecular Biophysics Lab, Department of Biotechnology

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