----- Original Message ----- From: shahab shariati <shahab.shari...@gmail.com> Date: Sunday, May 30, 2010 16:28 Subject: [gmx-users] separation of two strands of DNA during of simulation To: gmx-users@gromacs.org
> Dear Justin > > thanks for your attention. > > You said that separation of two strands of DNA during of simulation is a > normal consequence of periodic boundary conditions. I had used periodic > boundary condition in mdp file as following: No, he didn't say separation was a consequence of PBC. *Apparent* separation can be. I'm sure he provided this link, but make sure you read it, please :-) http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Mark > Periodic boundary conditions: > pbc = xyz > > Should I delete pbc from mdp file? > > Whether elimination of pbc prevents separation of two strand of DNA? -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
