zeroMomentum for SMD

From: Ihsan Omur Akdag (
Date: Fri Aug 20 2010 - 05:58:18 CDT

I am working on a membrane and peptide system. I am trying to pull the
peptide from outside of the membrane through the membrane. The peptide is
pulled with constant velocity steered molecular dynamics. However, when the
peptide moves through the membrane, the membrane starts to move in the
direction of the peptide. I used "zeroMomentum on" in the conf file for the
first simulations and in those simulations the membrane did not move which
is what I wanted. However, when I checked out the NAMD configuration
parameters, it is stated "This feature should only be used for simulations
that would conserve momentum except for the slight errors in PME. (Features
such as fixed atoms, harmonic restraints, steering forces, and Langevin
dynamics do not conserve momentum; use in combination with these features
should be considered experimental.)" What should I do?

Best regards,

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