AMBER Archive (2009)
Subject: Re: [AMBER] momentum in MD simulation
From: case (case_at_biomaps.rutgers.edu)
Date: Tue Sep 01 2009 - 06:48:52 CDT
On Mon, Aug 31, 2009, dhacademic wrote:
> I found that the center of mass of my system (PBC) will change after MD
> simulations by using PMEMD. So I check the momentum of the system. The
> total momentum of the whole system should be zero. But in my case, the
> momentum in x, y and z directions are all nonzero. What's wrong?
The argument that "the total momentum of the whole system should be zero"
needs to be treated carefully. If the initial velocities don't have zero
net momentum, then Newton's equations will preserve that, and you will see
a drift. If you are using a thermostat, there can be fluctuations in the
momentum due to that. In all circumstances, round-off errors can also
lead to non-zero momentum.
Your post doesn't give any details about what sort of simulation you are
running, or what the starting conditions were. Nor is it clear how far from
zero your momenta are. It's probably useful to run a small periodic system
where you can control these things, and to run experiments to identify the
important parameters. (Check the nscm parameter as well.)
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