[gmx-users] DNA simulation

delara aghaie d_aghaie at yahoo.com
Tue Dec 11 11:22:38 CET 2012

Dear Gromacs users

I want to simulate dobule strand DNA using gromacs. I have read that I should use amber forcefield for DNA simulation and I have crossed a web page explaining some parameters which I should change in gromacs package to become compatible with this amber force filed. 

1) I want to know that is it possible to use straightly pdb2gmx command on pdf file of DNA (taken fron protein data bank) and choose amber forcefiled for that? 

2) Are that changes necessary? 

3) If pdb2gmx does not give error how can I make sure about the correctness of procedure.
Thanks in advance
Regards D.M

More information about the gromacs.org_gmx-users mailing list