AMBER Archive (2009)

Subject: [AMBER] center of mass

From: dhacademic (dhacademic_at_gmail.com)
Date: Thu Aug 20 2009 - 15:50:47 CDT

Dear Amber users,

Langevin dynamics and implicit solvent are used in the simulations (NPT and PBC, room temperature) of polymer conformation. I have carefully heated and equilibrated the system and a 30ns trajectory has been accumulated. However, the center-of-mass of the whole system keeps on drifting. I have the following three questions:

(1) Is it normal that the center-of-mass keeps on drifting?

(2) If not, then what is the possible problem?

(3) If it is normal, then which one should I use to to calculate the diffusion constant of solute (the polymer chain): the absolute value of center-of-mass or the relative ones (I mean the relative displacement between solute and solvent)?

I have read the recommended paper, but I am still confused about this problem. Any suggestion is appreciated.

%A R.W. Pastor
%A M. Karplus
%T Parametrization of the friction constant for stochastic simulations of
polymers
%J J. Phys. Chem.
%V 92
%P 2636-41
%D 1988

2009-08-20

dhacademic
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