[gmx-users] LINCS

Stephen M. Dutz smdutz at csupomona.edu
Tue Jan 1 22:06:29 CET 2008

Hi all,

Will someone please explain to me why I am seeing the following...  I am running a protein/ lipid system with position restraints on the protein.  I run two identical runs except in one I have lincs-iter = 1 and the other I have lincs-iter = 4.  With lincs-iter = 1 I observe 26.0 hrs/ns computational time.  With lincs-iter = 4 I observe 4.0 hrs/ns.  This seems a bit backwards to me, but perhaps I have misunderstood something.

Other pertinent settings are; 2fs timestep, pbc = xyz, PME, berendsen thermostat and barostat @ 310K and 1 bar, constraints on all-bonds, Lincs constraint algorithm, lincs-order = 4

Thank you and Happy new year!


"You must be the change you want to see in the world."
-Mahatma Gandhi


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