[gmx-users] Re: DNA will not stay in the middle of the box (Nicolas)

Benjamin Woiczikowski p.woiczikowski at tu-bs.de
Thu Dec 11 15:35:22 CET 2008

Hi again,

I am aware that it is not quite physical to do so, but in this particular 
project it really helps to use such a protocol.

Indeed, it worked perfectly in 3.3, so why should that not work with 4.0? May 
there be a bug in 4.0?


>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 

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

Paul Benjamin Woiczikowski
Department of Physical and Theoretical Chemistry
Technische Universität Braunschweig
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