[gmx-users] elastic network model -protein contracting
Hi all, I want to prepare a basic elastic network model (tirion model) of protein. For this i have taken only C-alpha atoms of the protein and considered only streching potential(k.(b-b0)^2)) and removed rest of angle,dihedral,non bonded interactions. I have mentioned a bond between C-alpha and C-alpha in ffbonded.itp file with equilibrium distance 0.39 nm and force constant of 96400 kj/nm2 . I don't performed any minimisation ,just done equilibration and production. When i load final trajectory file(after production run) the protein contracts after first frame ,some of the atoms are over one another overlapping one over the other. Please help me to solve this problem. Thanks in advance, Mohan. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] elastic network model -protein contracting
On 22/08/2012 1:06 PM, mohan maruthi sena wrote: Hi all, I want to prepare a basic elastic network model (tirion model) of protein. For this i have taken only C-alpha atoms of the protein and considered only streching potential(k.(b-b0)^2)) and removed rest of angle,dihedral,non bonded interactions. I have mentioned a bond between C-alpha and C-alpha in ffbonded.itp file with equilibrium distance 0.39 nm and force constant of 96400 kj/nm2 . I don't performed any minimisation ,just done equilibration and production. When i load final trajectory file(after production run) the protein contracts after first frame ,some of the atoms are over one another overlapping one over the other. Please help me to solve this problem. Your model has no way to prevent overlap. You need to fix the model. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
