[AMBER] Is It Possible to Prevent Center-of-Mass Rotation During MD?

From: Logan Ahlstrom <logana.email.arizona.edu>
Date: Wed, 7 Jul 2010 19:41:47 -0700

In regards to the issue stated below, is there any way to prevent the
center-of-mass (COM) rotation of a molecule during simulation? I have
come-across the nscm flag, but this will only remove translational COM for
periodic simulations. Any suggestions would be much appreciated.


Logan S. Ahlstrom
University of Arizona
Department of Chemistry and Biochemistry
Miyashita Lab

I am currently running an explicit water REMD simulation of a dimer that
roughly has the shape of a “dumbbell”. Thus, when I solvate the system by
simply specifying a padding distance extending from the molecular
dimensions, a rectangle results. However, during simulation the molecule
rotates such that the long side of the “dumbbell” extends along the shortest
side of the rectangle and the protein becomes too close to its periodic
neighbors (i.e. within the the van der Waals and electrostatic cut-off I
have specified). As for now, the only way I can think to fix this problem
is to solvate my system in a large cube such that the length of each side is
greater than the length of the “dumbbell” plus the cut-off distance.
However, this dramatically increases the number of water molecules needed
for simulation.
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Received on Wed Jul 07 2010 - 20:00:03 PDT
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