Dear users, Although this topic has been extensively discussed in the list previously, I am unclear about the solution for the problem..
While running ligand in water simulation (EM) with RF-0 I get the following message: ---------------------------------------------------------------------------------------------------------- Number of degrees of freedom in T-Coupling group rest is 24531.00 Largest charge group radii for Van der Waals: 0.458, 0.356 nm Largest charge group radii for Coulomb: 0.458, 0.356 nm NOTE 1 [file ../em.mdp]: The sum of the two largest charge group radii (0.814337) is larger than rlist (1.600000) - rvdw (1.000000) NOTE 2 [file ../em.mdp]: The sum of the two largest charge group radii (0.814337) is larger than rlist (1.600000) - rcoulomb (1.400000) ---------------------------------------------------------------------------------------------------------- But I continued for nvt and npt where I got the same notes NVT - ---------------------------------------------------------------------------------------------------------- Largest charge group radii for Van der Waals: 0.509, 0.487 nm Largest charge group radii for Coulomb: 0.509, 0.487 nm NOTE 1 [file ../nvt.mdp]: The sum of the two largest charge group radii (0.996343) .... NOTE 2 [file ../nvt.mdp]: The sum of the two largest charge group radii (0.996343) ..... ---------------------------------------------------------------------------------------------------------- for NPT - Number of degrees of freedom in T-Coupling group System is 16357.00 Largest charge group radii for Van der Waals: 0.787, 0.684 nm Largest charge group radii for Coulomb: 0.787, 0.684 nm NOTE 1 [file ../npt.mdp]: The sum of the two largest charge group radii (1.470764) ..... NOTE 2 [file ../npt.mdp]: The sum of the two largest charge group radii (1.470764) ..... ---------------------------------------------------------------------------------------------------------- For MD - ---------------------------------------------------------------------------------------------------------- Largest charge group radii for Van der Waals: 0.671, 0.605 nm Largest charge group radii for Coulomb: 0.671, 0.605 nm NOTE 1 [file md.mdp]: The sum of the two largest charge group radii (1.276104) ...... NOTE 2 [file md.mdp]: The sum of the two largest charge group radii (1.276104) ..... ---------------------------------------------------------------------------------------------------------- The ligand is not broken, whole of it is inside the water in the beginning of the simulation, topology is ok because protein-ligand simulation with PME ran fine. Any suggestions are welcome. Thank you Regards kavya -- gmx-users mailing list gmx-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