Dear gromacs users, I have done energy minimization of clustered PDBs. When I try to calculate the RMSD between the minimized clustered PDB and the starting structure of MD simulations I got the following warning.
If there are molecules in the input tarjectory file that are broken across periodic boundaries, they cannot be made whole (or treadted as whole) without you providing a run input file. I did not get what does it mean. I have not get any output for RMSD. Where I did wrong? Kindly tell me. Thanks in advance Surya Graduate student India. -- 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.
