[gmx-users] About the output information

[Justin Lemkul]

On 10/30/14 2:02 AM, Vinson Leung wrote:
> Hi all.
> I am new to gromacs and my major is not related to molecular simulation so
> I do not  know the meaning of almost everything in the output information :(
>
> For example, in the output file like below:
> =========================================================
> step  375: timed with pme grid 80 80 64, coulomb cutoff 1.089: 131.6
> M-cycles
> ....
> imb F 29% pme/F 1.25 step 1900, will finish Thu Oct 30 12:05:34 2014
> .......
>
> vol 0.80  imb F  3% pme/F 1.21 step 30100, will finish Thu Oct 30 12:05:27
> 2014
> ==========================================================
>
> what does "coulomb cutoff 1.089: 131.6 M-cycles", "imb F 29%","pme/F
> 1.25","vol 0.80" mean?
>

These are technical details related to cutoff tuning to get maximum performance, 
force imbalance for the DLB algorithm, and some notes about domain 
decomposition.  They're usually irrelevant unless you're trying to diagnose a 
problem.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================