[gmx-users] LINCS

Stephen M. Dutz smdutz at csupomona.edu
Wed Jan 2 19:48:50 CET 2008

Hi Mark,

Thanks for the reply.  I accidentally had lincs-iter set to 4 initially because I forgot to change it to 1 after minimization.  After looking into the issue some more I determined the odd results to be due to a few stray processes running on the node I was performing the calculation on.  After taking care of these stray processes the calculation time returned to  an understandable 3.8 hrs/ns.

Thanks again,

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.

Over how long were you measuring these performance times? You'll need a
few picoseconds to be sure you're not being dominated by setup time.

> 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

Use gmxcheck to compare your .tpr files to verify that the differences
you think exist are all that does exist.

Since you're not doing NVE, why do you want lincs_iter > 1?


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


More information about the gromacs.org_gmx-users mailing list