[gmx-users] Pull code with shuffle/sort options

Chris Neale chris.neale at utoronto.ca
Thu Aug 9 21:43:28 CEST 2007

>I have encountered noticeable differences while using the pull code with 
>the -shuffle -sort options in parallel, as opposed to running in serial 
>or in parallel without the options. Using -shuffle -sort, the dynamics 
>of the molecule of interest appears to be unaffected by the pulling 
>potential. Without the options, the molecule can be seen to be correctly 
>pulled in the desired direction. I'm using version 3.3.1, and this 
>problem is present in both single and double precision versions.

I recall that this is also the case for position restraints and a shuffled or sorted run. I believe that this is a known issue and that there is no solution. However, I can't remember where I read that I didn't find it either with a quick search of the mailing list and the manual fo things like posre shuffle or restraint shuffle

More information about the gromacs.org_gmx-users mailing list