[gmx-users] CHARMM36 in Gromacs :DNA terminus residues

Dear all, I am trying to do MD simulation on my protein-DNA system in *Gromacs* using *CHARMM36* force field (*2019 version*, downloaded from Mackerell web homepage). The DNA residue names start from DG5 ==> DC3 (in both DNA strand): Once I do *pdb2gmx* command, seems it does not correctly

[gmx-users] How restrain the end-to-end distance in simulation?

Dear all, I am new in Gromacs and would like to restrain the the end-to-end distance of a bend DNA. I mean I want to restraint the distance between COM of end base-pairs in simulation. I would appreciate if you could let me know how to do that. Cheer, Mahdi -- Gromacs Users mailing list *

[gmx-users] Adding residue at two end of DNA

Dear Gromacs User, Do you know how can I add some residue to ends of DNA? I am looking forward hearing of you,= Mahdi Bagherpoor -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read