[gmx-users] pair of amino acid

David spoel at xray.bmc.uu.se
Mon Mar 29 21:54:01 CEST 2004

On Mon, 2004-03-29 at 20:05, Amol Mungikar wrote:
> Dear Gromacs users,
> I was trying to do MD on a pair of amino acids. With only LJ params
> and no charges, the system does not reach equilibrium. When I include
> the charges, the system does go to equilibrium. Is this because of
> highly anisotropic nature of the system. Kindly let me know if anybody
> has done this kind of calculations before or maybe if anybody knows of
> any references.
if you just turn off part of the interaction the force field is not
balanced anymore, and you get nonsensical results. that doesn't mean it
is useless to do this, but you have to know what you're doing.
check the energies of a pure water run, and imagine what would happen if
your turned of the coulomb.

> Thanks you very much for your time.
> Amol
David van der Spoel, PhD, Assist. 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

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