PBC Wrap + TMD

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Mon Oct 10 2011 - 14:02:58 CDT

Dear NAMD list and developers,

I am running a TMD simulation (using NAMD 2.7) with a protein/ligand
complex. The targeted atoms include atoms of the protein and the ligand as
well. When the ligand approaches the edge of the box it is wrapped around,
as it is normally done in a MD simulation, while the protein is still in
its original location and not wrapped around. When the simulation restarts
from a restart file, there are huge forces applied onto the ligand which
cause the simulation to crash.

I think the problem is that the TMD module uses the coordinates of the
ligand contained in the primary cell instead of using those in the nearest
image. This causes huge forces to be applied onto the ligand and the
simulation to crash with errors from RATTLE.

Right now, I am avoiding the crash by turning off wrapAll and using
wrapWater only.



Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                     +1 (206) 685 4435

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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