Dear All, In my initial protein pdb structure I have added some external ligand molecules and as a result of that there are several short contacts. So, well, I minimized the system and then got the 'prot_min.gro' file. Now after the equilibration run, I plotted the RMSD of the resulting trajectory with respect to the initial pdb structure. So as the pdb had some short contacts, the resulting RMSD is showing large increasing value around 0.4-0.5 nm.
1) Then, is it better to plot [ for reporting purpose ] the RMSD of the trajectory with respect to the minimized coordinate file rather than w. r. t. the initial PDB file? 2) What is the acceptable range of RMSD for a protein simulation ? ( below 0.2 nm !! ) Thanks -- Tarak -- gmx-users mailing list gmx-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
