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

[Benjamin Woiczikowski]

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?

Regards,
Ben

>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 
>that.
>
>Regards,
>Nicolas


>> 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 
and 
>> at the end the DNA doens't stay in the middle of the box.
>>
>> Can somebody help?
>>
>> Regards,
>> Ben
>>  
-- 


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