Mark.Abraham at anu.edu.au
Wed Jan 2 00:10:30 CET 2008
Stephen M. Dutz wrote:
> 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?
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