[gmx-users] DNA will not stay in the middle of the box

Nicolas nsapay at ucalgary.ca
Thu Dec 11 06:09:35 CET 2008

Benjamin Woiczikowski a écrit :
> Hi,
> I simulate DNA molecules in water with counterions. To keep the DNA in the 
> middle of the box I had the following options in the input file:
> comm_mode = angular
> comm_grps=dna
I think this question has been already addressed for proteins. Anyway, 
removing the COM motions of only one component of your system is very 
probably a bad idea. You should rather use position restraints. If you 
look in the mailing-list or the manual, you will quickly find how to do 

> For the old version (3.3.2) it worked but now (4.0.2) there are warnings and 
> at the end the DNA doens't stay in the middle of the box.
> Can somebody help?
> Regards,
> Ben

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