[gmx-users] Question about MD simulation

Dear gromacs users, I have a quetion regarding using amber forcefield in gromacs. I did the DNA and water interaction simulation. After the energy minimization, the original helix-structured DNA becomes two fragments. At this stage, I assume that the simulation process is correct. I used exactly

Re: [gmx-users] Question about MD simulation

You want to name the atoms according to the atom types in ffamberXX.rtp file. For an example of this for DNA see the dickerson.pdb provided in the README directory of the ffamber port or this pdb can be downloaded on its own from: http://folding.stanford.edu/ffamber/ Tom --On 30 May 2007