[gmx-users] hello

[Mark Abraham]

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.

See 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Mark
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120618/1db3713a/attachment.html>