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
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