[gmx-users] webpage for searching gromacs mailing archive
Hi I used to find the link for searching the previous posted discussions and all the threads in the gromacs home page where there used to be a 'search' option for looking for discussions on a topic. But, now, looking for the same archive in Mailing Lists - Gromacs redirects me to gromacs home page where I can not find anything on the archive. I will appreciate if someone can redirect me the right webpage. ThanksSanku | | | | | | | | | Mailing Lists - GromacsLog in Register Gromacs Support Bugs and Feature Re... Mailing Lists GMX-Developers List GMX-Users List The gmx-announce Li... The gmx-revision Lis... Online Manual Workshops Mailing Lists | | | | View on www.gromacs.org | Preview by Yahoo | | | | | -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Time averaged ramachandran plot
Hi I plan to plot the ramachandran plot of all the dihedral angles each of which is averaged over time-frames of trajectories. But, I find g_rama or g_chi gives the time profile of ramachandran plot. But, if I want to plot the time-averaged Phi.Psi angles of all residues, is there any method to do it.ThanksSanku -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] treatment of electrostatics in vaccum
Hi I need to run MD of a charged macromolecule in gas-phase or in vaccum. I was wondering if I use no periodic boundary condition ( i.e. setting pbc=no and ns_type=simple), can I get away with non-ewald type electrostatics method ( i.e. by using a very large cut-off like 3 or 4 nm for electrostatics ) ? In this case, I wanted to minimize the computing expense associated with PME electrostatics. Thanks Sanku -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] angle between benzene rings
Dear gromacs users I would like to compute the angle of orientation between two benzene rings that I have simulated using gromacs. I think, for this, I have to get the vector normal to the plane of the benzene ring and then get the angle of among the unit vectors. Is there any tools in gromacs that can help me to do this? Does g_sgangle work here? Sanku -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] counter ion and charged polymer in gas-phase
Hi, I am doing simulation of charged polymer . When I do the simulation in water or solvent, I put counter ion in the solvent to neutralize the charge in the system. But, if I want to do the simulation in gas-phase ( i.e no solvent), does adding counter-ion make any sense or is it realistic? I mean : does counterion remain present in gas-phase ? Or, should I use charged system which might get neutralized by back-ground neutralizing effect of Particle-Mesh Ewald? Thanks Sanku -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
