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

Steve Fiedler fiedler at umich.edu
Fri Aug 10 15:34:27 CEST 2007

Thank you Chris for providing recognition of this issue. 


Chris Neale wrote:
>> 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

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