[gmx-users] about ending basepairs in DNA simulation

[Mark Abraham]

On 6/04/2010 11:51 PM, Wu Rongqin wrote:
> Dear all,
> 
> I am doing simulation on a short B-DNA which containing 11 basepairs. My 
> interest is on the middle basepair in the sequence. During the 
> simulation, I found severe distortion on the two basepairs at both ends, 
> for example, the dihedral angle deviates from 180 degree severely.
> 
> Must I put any restraint to the basepairs on both ends so that I can 
> simulate a basepair in a long sequence?

That would at least depend on your force field, which you haven't told us.

> Please give me some advice if you can.

We can't really, since you haven't told us your force field, or how
you've prepared your termini, etc.

Mark