Re: [gmx-users] Topology- make bonds with certain cut-off distance

On 25/08/2012 11:58 PM, mohan maruthi sena wrote: Hi , Thanks for your reply. I actually want to build an elastic network model (ENM) for Protein containing 372 residues. According to literature, ENM model only considers C-alpha atoms of protein and discards rest of the atoms.The potential

Re: [gmx-users] Topology- make bonds with certain cut-off distance

Hi , Thanks for your reply. I actually want to build an elastic network model (ENM) for Protein containing 372 residues. According to literature, ENM model only considers C-alpha atoms of protein and discards rest of the atoms.The potential only considers bonded term only. It does not contain

Re: [gmx-users] Topology- make bonds with certain cut-off distance

Hi, In case you want the "bonds" to be dynamic I think the only way is to use tabulated interactions. A bit tedious to set up, but doable. Note that this will NOT emulate angles or dihedrals, just the stretching term. I can't understand why you would want bonds between all atoms within a certai

[gmx-users] Topology- make bonds with certain cut-off distance

Hi all, I want build a toplogy for a protein , for which , each and every atom has to make bonds with other atoms with in certain specified cut-off distance. How can i do this ? Please suggest me a way, Thanks in advance, Mohan -- gmx-users mailing listgmx-users@gromacs.org htt