[gmx-users] Re: Re:unexpected large difference in potential energy calculation by different method: cut-off and switch

Dongsheng Zhang dong at pampas.chem.purdue.edu
Thu Dec 1 21:07:36 CET 2005

Dear David,

Thank you for your reply. When I read your email at the first time. I
think you have answered my question. But when I think it again today, I
find I still have a question:

I can understand that there will be some artifacts to calculate forces
by using switch function in MD simulation because switch function only
smooths the potential. My question is: If I calculate the total
potential energy of a system by rerunning a trajectory file with two
different methods (Cut-off and switch), should I get close results
because I don't need to calculate the force to determine the next
configuration of the system? 

Dongsheng Zhang wrote:
> Hi, > > I am comparing different methods to calculate the coulomb and VDW
> potential energy. I think the results for cut-off and switch should be
> close. However, the difference is very large. Could anyone tell me what
> happen? Detailed information is as follows:

Switched potentials should be avoided. In GROMACS the switch is atom 
based which gives huges artifacts, in other codes you can choose group 
based switches which has less artifacts but introduces a horrible 
arbitrariness in the definition of the groups. For more info see:

The Origin of Layer Structure Artifacts in Simulations of Liquid Water
David van der Spoel and Paul J. van Maaren, in press
J. Chem. Theor. Comput. http://dx.doi.org/10.1021/ct0502256

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
Dongsheng Zhang <dong at pampas.chem.purdue.edu>

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