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

[David van der Spoel]

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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