[gmx-users] hello

Mark Abraham Mark.Abraham at anu.edu.au
Mon Jun 18 11:56:24 CEST 2012

On 18/06/2012 7:46 PM, Anik Sen wrote:
> Hi This is Anik.

Please choose an email subject more descriptive of your problem. That's 
your chance to attract attention!
> Am using Gromacs 4.5.5 for running dynamics of a DNA surrounded with 
> water. The DNA consisted of a total 10 base pairs. But within the 
> simulation the DNA is moving inside the solvation box and sometimes it 
> is going outside of the box, though due to NVT simulation criteria the 
> part going out from one side comes back from the other side. But the 
> problem is in a certain step it looks awkward that part of DNA lying 
> here and part lying there. I have taken bigger boxes but with the same 
> result.
> Can anyone suggest how to overcome this problem? The interaction of 
> the DNA with the water molecules may not hamper but it may not dance 
> so much in the solvation box.


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