[gmx-users] LINCS Warnings in the middle of an MD run

David van der Spoel spoel at xray.bmc.uu.se
Fri Dec 14 11:16:01 CET 2001

On Fri, 14 Dec 2001, K.A.Feenstra wrote:

>[.. after reading David's comment, I felt I could add something more...]
>This is a 'normal' error, in the sense that a rotatable group like
>your protonated NH3 group in the lysine sidechain, can build up a large
>rotational velocity. Since this motion couples only weakly with the
>rest of the system, once you have the high rot. velocity, it stays there
>for some time. If the velocity builds up too high, lincs will get problems
>re-setting the bond lengths that get elongeted due to centripetal forces.
>There is a finite chance to get this buil-up, which obviously increases
>with simulation length...
I'm not entirely convinced. The NH3 should probably be hydrogen bonded to
something, and in that have quite strong forces on them. Furthermore there
is also a weak dihedral force (which is periodic of course). The only way
in which such rotation could be maintained is when it rotates by 120
degrees (around the CE-NZ torsion) in one step. In that case
electrostatics does not change. However, that seems quite unlikely to
me... As a remedy maybe one could increase the torsional barrier, or
obviously use shorter timesteps...

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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