[gmx-users] Principal Component Analysis (PCA)
hi all, Can we plot RMSF versus atom numbers using eigenvectors of a different simulation and trajectory of another simulation. I know we can plot RMSF versus atom numbers using the eigenvectors and trajectory of a same simulation using g_anaeig Thanks in advance -- View this message in context: http://gromacs.5086.n6.nabble.com/Principal-Component-Analysis-PCA-tp5003246.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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
[gmx-users] Energy minimization with walls
Hi all, I am simulating a box filled only with water and having walls at Z=0 and Z=Z_box. I am confused that whether energy minimization process removes the bad contacts between wall atoms and solvent or not ? any kind of help would be really appreciated -- View this message in context: http://gromacs.5086.n6.nabble.com/Energy-minimization-with-walls-tp5003229.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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
[gmx-users] Creating layers of atoms in the BOX
Dear all, I am a final year undergrauate student and a novice in GROMACS. I want 3-4 layers of Carbon atoms to be added one over the other in my box starting from Z=0 to Z=(3-4 carbon diameter). How can I do that. Please help me out -- View this message in context: http://gromacs.5086.n6.nabble.com/Creating-layers-of-atoms-in-the-BOX-tp5002697.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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
[gmx-users] are wall atoms virtual ?
Dear all, My system consists of Two walls of carbon atoms but I am not able to view the carbon atom walls in VMD. Also my topology file have no information about wall atoms. So is it possible to see them somehow or my system has no walls indeed ? -- View this message in context: http://gromacs.5086.n6.nabble.com/are-wall-atoms-virtual-tp5002549.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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
