[gmx-users] Protein-surface interaction during flow

Smith, Micholas D. smithmd at ornl.gov
Tue Jan 31 17:18:29 CET 2017

Christopher makes a good point.

Thermal motion will likely take over, but if you use a long enough initial push, you should also induce a local velocity field in the solvent around the protein which will allow some drifting. Alternatively you could give a kick to both the solvent and protein.

Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Christopher Neale <chris.neale at alum.utoronto.ca>
Sent: Tuesday, January 31, 2017 11:15 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] Protein-surface interaction during flow

flow the solvent and let the protein respond freely to that?

My guess is that the initial velocities will be lost fairly quickly to thermal noise if you try the suggestion of giving it a kick and then simply letting it go.

— original message —

I am trying to simulate a flow of protein over and along a surface
structure. To do this, I have a box which is very long in its x
direction, relatively small in its y direction and its z dimension is
limited by an artificially created surface. These proteins will move
in the positive x direction, starting at around x=0, and move towards
the surface structure. At this point the protein will either pass
along the structure, or adhere to it through LJ/Coulomb interactions.
There will also be interactions between the (many) proteins flowing.
Essentially, I’m trying to create a flow.

However, I’m unsure on how to do this. If I set the proteins as a
acc-grps, they will continue to accelerate even after they have
adhered to the surface, essentially pulling them off. Is there a way
to set acc-grps for a specific amount of time or distance? After which
their velocities will guide them towards the surface structure? Or can
I give these proteins a starting velocity after which they just flow?
Any ideas?

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